diff options
Diffstat (limited to 'sci-biology')
721 files changed, 35478 insertions, 0 deletions
diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild new file mode 100644 index 000000000000..a86386004736 --- /dev/null +++ b/sci-biology/ApE/ApE-2.0.7-r1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +DESCRIPTION="A Plasmid Editor" +HOMEPAGE="http://www.biology.utah.edu/jorgensen/wayned/ape/" +SRC_URI="http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ${P}.zip" + +LICENSE="ApE" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="app-arch/unzip" +RDEPEND=" + dev-lang/tcl:0 + dev-lang/tk:0" + +RESTRICT="mirror" + +S="${WORKDIR}/ApE Linux/" + +src_compile() { :; } + +src_install() { + cat >> "${T}/ApE" <<- "EOF" + #!/bin/bash + cmdArgs="" + + # AppMain.tcl searches files relative to the directory where it resides. + # Add absolute path to file here, if necessary. + for rfpath in "$@"; do + afpath="$PWD/${rfpath}" + if test -r "${afpath}"; then + cmdArgs="${cmdArgs} \"${afpath}\""; + else + cmdArgs="${cmdArgs} \"${rfpath}\""; + fi + done + + eval exec tclsh "\"/usr/share/ApE-2.0.7/AppMain.tcl\"" "${cmdArgs}" + EOF + + dobin "${T}/ApE" + insinto "/usr/share/${P}" + doins -r "${WORKDIR}"/ApE\ Linux/* + make_desktop_entry ${PN} ${PN} \ + "/usr/share/${P}/Accessory Files/Icons and images/monkey_icon.gif" \ + "Science" +} diff --git a/sci-biology/ApE/Manifest b/sci-biology/ApE/Manifest new file mode 100644 index 000000000000..c6024d647ae1 --- /dev/null +++ b/sci-biology/ApE/Manifest @@ -0,0 +1,5 @@ +DIST ApE-2.0.7.zip 318454 SHA256 9d718562ef250b68dfad1de7d4179540fc04c001b0fdc5e9bd70f3605561bc32 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254 WHIRLPOOL d13e8a997c36f8e7ac951a17c195a714a243292f9a99f524758b09b1fdc9f436b11cf1124ac1a3527ff70aa8cc6dc9ac516a910246f9f6e4f8376c78e8b44013 +EBUILD ApE-2.0.7-r1.ebuild 1170 SHA256 7384c2cc9eeb2a5be2d2f5c666bb0863e96662facccd5d24d0c54f67ea2dc3de SHA512 7260638810e5ef22da0b07f05e3046451e3b3a581706326caa073ff49255a36770cd622cbd0c428010fb39950b54248aa6112f8aa525260d8ebd312bc21d75ab WHIRLPOOL 333a557c28960b108c3879e9a78d859677ba33dc4f7c5a854fcae331ca118c1faf79199cb4f44d405c570251aefdc2f96b4159b566195e307676ea7171b745bb +MISC ChangeLog 2294 SHA256 b84ab03703ae606925d2afe2040749655e151401301ffed6f074fd1d18e0e653 SHA512 f8df638de8b147a180ee9f150a134abad76a58f20fcac2249995f0b7ef6b93bd31a469644253119301516c992f43496e477ce5cde33e3c5fc869dcbc1d16c757 WHIRLPOOL 18ebe7545252f1b8aedc7e712d6a134613ac3435412b95c48b3d8549deccbbb806f7776780e8f204ab6b6dcaf53086b2bf167893a113286ffce187cba9d89a4d +MISC ChangeLog-2015 1681 SHA256 ed4f99c5e1c819ad466daf75129d3f88c11997a4692a9a4f6287fa2a7d627578 SHA512 d0f2f54e7cdf3778d6afa724899360a2148ecc26d1e4147fd406e28bf595764edefcf021232a2a7e0fc8531596ce190abd0348258975e72716ab0cbae8b24cbe WHIRLPOOL 858889149946910622afde6a802553fbc50a9d75b800406a84beb0ba73df373a5782637f4c46e60daed246c8e364c5b8f002245f15f5a47445131103a6c8bdd0 +MISC metadata.xml 139 SHA256 5cdc1888ebc8807b9a37b1d33429c61cabe7415a4f240e21a4c2ff8eca7a34ed SHA512 8be912ace7468a4396eb1da00a9785030a8ce35da4357a01591876a1056fd45e44da65de2af3e1eb0506ce6551714962c40c3ae5a3aefa2ad231de35af2519be WHIRLPOOL 620431014dd4fb752c3d46d11904ecb2c6d4525f5b4e30f4f778a3b74d3f7187ae4ccd856ebd7eabb48ce261b21849c732928fe647edce024a3fdc082d8f8630 diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml new file mode 100644 index 000000000000..097975e3adc2 --- /dev/null +++ b/sci-biology/ApE/metadata.xml @@ -0,0 +1,4 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +</pkgmetadata> diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild new file mode 100644 index 000000000000..739950568156 --- /dev/null +++ b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +MODULE_AUTHOR=LDS +inherit perl-module webapp + +DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser" +HOMEPAGE="http://gmod.org/wiki/GBrowse" +KEYWORDS="~amd64 ~x86" +IUSE="-minimal mysql postgres +sqlite" + +SLOT="0" +WEBAPP_MANUAL_SLOT="yes" + +CDEPEND="!<sci-biology/GBrowse-2.44-r1 + >=sci-biology/bioperl-1.6.9 + >=dev-perl/Bio-Graphics-2.09 + >=dev-perl/GD-2.07 + >=dev-perl/CGI-Session-4.02 + dev-perl/IO-String + dev-perl/JSON + dev-perl/libwww-perl + dev-perl/Statistics-Descriptive + !minimal? ( + dev-perl/Bio-Das + >=dev-perl/Bio-SamTools-1.20 + dev-perl/Crypt-SSLeay + dev-perl/DB_File-Lock + dev-perl/DBI + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sqlite? ( dev-perl/DBD-SQLite ) + dev-perl/FCGI + dev-perl/File-NFSLock + dev-perl/GD-SVG + dev-perl/Net-OpenID-Consumer + dev-perl/Net-SMTP-SSL + )" +# >=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile +DEPEND="dev-perl/Module-Build + dev-perl/Capture-Tiny + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch ) + +src_configure() { + webapp_src_preinst + +# myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse" + myconf="--conf=/etc/gbrowse2" + myconf="${myconf} --htdocs=${MY_HTDOCSDIR}" + myconf="${myconf} --cgibin=${MY_CGIBINDIR}" + myconf="${myconf} --tmp=/var/tmp/gbrowse2" + myconf="${myconf} --persistent=/var/db/gbrowse2" + myconf="${myconf} --databases=/var/db/gbrowse2/databases" + myconf="${myconf} --installconf=no" + myconf="${myconf} --installetc=no" + perl-module_src_configure +} + +src_install() { + dodir /var/tmp/gbrowse2 + dodir /var/db/gbrowse2/sessions + dodir /var/db/gbrowse2/userdata + webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2 + perl-module_src_install + webapp_src_install +} diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest new file mode 100644 index 000000000000..451cb18308f9 --- /dev/null +++ b/sci-biology/GBrowse/Manifest @@ -0,0 +1,6 @@ +AUX GBrowseInstall.pm-2.39.patch 2878 SHA256 80a1aefac21c55c040e89028f736c058b35695cbb816e44f4465665cdd14f9ab SHA512 637dea799290213def1368cdb153463c96964ada99fd6c09d0b95e0d1e42a16942d66ef36282d39b92284ae6eb26c8346d5ad1289b5ec7b2196a1ba5090db85e WHIRLPOOL 8d09777c778865a1df29dd347befddcfa5399433ab1caaaa9d519895716612d1b8ae8e10f3d21b261d39aa65f26df18535ed6dc6db76bb1488e7eab13f3194e7 +DIST GBrowse-2.48.tar.gz 11958127 SHA256 02772c5a7a31ed87733e21278efec2edd3bd6ee8a4bec9b002233e57f6dc9681 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db WHIRLPOOL 5a3ec31de1582c4c551c76908ca8e8024c8d3311404f0c94f7b75a391c340da0ededd80df34be3f10f581902ba1408d84e3e65218f46322546623e15a1020135 +EBUILD GBrowse-2.48-r1.ebuild 1863 SHA256 0c02849fccbdef91a1a63182b82856937ccdaddcbd2057ec2e70bd860037132f SHA512 5ca80f79071c4312c0f79ef05855d5928b47973a068bcf573296c97367f79091fc686dfa474795c2ec7b89573333de91b63b0d51d316cbcfc24a618f16dc5cd8 WHIRLPOOL abc518243534974da5bf544ce5a70408bc4d3fc764d4c835be701d2697f11f1c0b3ebafc92dc2f969acbb9f7bfb612c0ac4c2d053af94167db19f42183af0665 +MISC ChangeLog 2471 SHA256 dd324c08338a59f49764c479511dd4705ed95b8878954d8ba1d643c8d06ce669 SHA512 f2952d424a125d217adeb8bbd89836ea088e078400a6598c67ad19854de23fb6239e4ecb587887940609e48b6eb9449c304df0168ee1fee72401349778faf55c WHIRLPOOL bc5664af0b6ea51b38990edfaee23800c3659aaea3c176b917ba5ab754170a0574c01f8deac66fb6ac68f8641fa79b1979255c6fc0fd899c6e8069407742e229 +MISC ChangeLog-2015 1747 SHA256 b6e74ca4c0bab66ba47f2c1dd0639bfc87e907fb6e5200ea2eaf2aca249645a2 SHA512 f0f941e64f638ba51dd1a35d6aa195ec56cf965850115da620c7c98cc1839b2dcd7456c5ee4f25c29b99effed001e1dee169abe63a193d0832852add776ee5ef WHIRLPOOL 5b659b75c1324bc69632978a52dc3e5ff9f6d7399f967809e9bbbb520196f067ffcc5d463359c140337e66451f81bd4adf5007368e231a2e4c1f7f4e7d17264d +MISC metadata.xml 327 SHA256 150c9f7958bd83e5f82936bad19974d2b677da3c0e6e13035d8af870850118a0 SHA512 12bed277a17513c5e45f782c500c6aa4cbaad988ffb902220dbacde7e908246a62663b976a822c63a5446306ad705ad27c504713dd61e7cf90dd23ce37d98e48 WHIRLPOOL 83bde0f26dd7cbd4b430746f92a05a4f3d7f7448bc9eb14911b8958215426504b2081fbea818eb8ef4a63eac4e8428c5247446b861a025f8bc62678f0d1bf5e1 diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch new file mode 100644 index 000000000000..5aa0be9df918 --- /dev/null +++ b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch @@ -0,0 +1,72 @@ +diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm +--- GBrowse-2.39-orig/install_util/GBrowseInstall.pm 2011-07-19 20:14:52.434608020 +0000 ++++ GBrowse-2.39/install_util/GBrowseInstall.pm 2011-07-19 21:02:13.685107753 +0000 +@@ -454,33 +454,33 @@ + $gid =~ /^(\d+)$/; + $gid = $1; + +- unless (chown $uid,$gid,$tmp) { +- $self->ownership_warning($tmp,$user); +- } ++# unless (chown $uid,$gid,$tmp) { ++# $self->ownership_warning($tmp,$user); ++# } + + my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); + my $images = File::Spec->catfile($tmp,'images'); + my $htdocs = $self->install_path->{htdocs}; +- chown $uid,-1,$htdocs; ++# chown $uid,-1,$htdocs; + { + local $> = $uid; +- symlink($images,$htdocs_i); # so symlinkifowner match works! ++# symlink($images,$htdocs_i); # so symlinkifowner match works! + } +- chown $>,-1,$self->install_path->{htdocs}; ++# chown $>,-1,$self->install_path->{htdocs}; + + my $persistent = $self->install_path->{'persistent'}; + my $sessions = File::Spec->catfile($persistent,'sessions'); + my $userdata = File::Spec->catfile($persistent,'userdata'); +- mkpath([$sessions,$userdata],0711); ++# mkpath([$sessions,$userdata],0711); + + my $databases = $self->install_path->{'databases'}; + +- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { +- $self->ownership_warning($databases,$user); +- } ++# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { ++# $self->ownership_warning($databases,$user); ++# } + +- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); +- $self->fix_selinux; ++ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); ++ # $self->fix_selinux; + + my $base = basename($self->install_path->{htdocs}); + +@@ -489,14 +489,14 @@ + my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); + my $perl = $self->perl; + my @inc = map{"-I$_"} split ':',$self->added_to_INC; +- system $perl,@inc,$metadb_script; +- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; ++# system $perl,@inc,$metadb_script; ++# system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; + +- if (Module::Build->y_n( +- "It is recommended that you restart Apache. Shall I try this for you?",'y' +- )) { +- system "sudo /etc/init.d/apache2 restart"; +- } ++# if (Module::Build->y_n( ++# "It is recommended that you restart Apache. Shall I try this for you?",'y' ++# )) { ++# system "sudo /etc/init.d/apache2 restart"; ++# } + + print STDERR "\n***INSTALLATION COMPLETE***\n"; + print STDERR "Load http://localhost/$base for demo and documentation.\n"; +Only in GBrowse-2.39/install_util: GBrowseInstall.pm~ diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml new file mode 100644 index 000000000000..1473cc001b3d --- /dev/null +++ b/sci-biology/GBrowse/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> +</maintainer> +<upstream> + <remote-id type="cpan">GBrowse</remote-id> +</upstream> +</pkgmetadata> diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest new file mode 100644 index 000000000000..78f05182f5ed --- /dev/null +++ b/sci-biology/aaindex/Manifest @@ -0,0 +1,5 @@ +DIST aaindex-9.1.tar.bz2 133780 SHA256 ae2e5aec2fc47835f26c8d8b5776966464bc08a5fca422c130d8312880382caa SHA512 d35760712a3f9d8c0d64e32ff450802eab20294851e569cbb9614610704f687c9ec56c440e6009b5c75c45ae12bd7968e28afcc414309318e94b092507df16d8 WHIRLPOOL c0bd3b3aa6ee730b5663f5b5c2be31925431d9f0a42488f2d2162e0d887f5ccc449c356f1c814854a0db2d48907763d586926ba14bbf3c277a006bb7f6b2fe4e +EBUILD aaindex-9.1-r1.ebuild 967 SHA256 1f33080cbbd5ba79a0ac9fa522b06872c9c0fc901453a5aa91c0f449b49836d7 SHA512 97b5c262baaa4bec1f0d32d3f343252862f5f2510cf6c4972e63d500fcc6169a8eb8e62d1f0e64f0f4ff5c2b90cbfeb24abbbc676d1c05701f092e520d7ac490 WHIRLPOOL 4f8153b4f6cf870c0928abc1efb0343829b3a5ac83dc3899e2cae41f69a655fbedbf8e323c53a0181ed35e16b5f42a3844d32f0b008c74c4a69833bda37621ab +MISC ChangeLog 2426 SHA256 1c2d7d20816e49468ac55e807a26b47aec49fc8a2219ddb769355c3fb09c60d0 SHA512 202c6d23baa93d0b18c915b924055015f7a2cd2dd803bb74faa17bac2d51d16f5b7e6c7fc7d421c49a49f0c1474b53f0cedf1f2eabe18b70847a94e085ad25e2 WHIRLPOOL 55c83b6ddb125ce870cf9f6b6fb93794cd34887afc1d4ba3719de3d99ab9d3eb11fd13806599b0dded8e13364f6c244bf7edac4983fc1874591c1fb58adbc6ce +MISC ChangeLog-2015 3444 SHA256 d61bd3519476b3a4f0868d426c463cd28c7a3940fa9b1ae53c3a2bae383c07db SHA512 bde79cf2580cfedd9db9cdd6ab88c5c2984c92987a07e6c37b04d0d93534462fc4816486b9abfc8ff09550c4e5b6c08b6f7a4b273a73f360011e53900a9aac90 WHIRLPOOL 45b527594321c95635d859a368d86a428ce29c5f2c9b6a315973f711a79b4199c8a1253a5722f3b56423d64420eeb30b8f882bbbacb614fa7a0f6e6e5153095d +MISC metadata.xml 1317 SHA256 526f2b21a5bfa52c18f4e6c67eba1e23699866d0a9c9ec5ac0cb4723a1432b10 SHA512 34360f262abb6d882e95272da0102519c75fac4a367c1e122cb91f3a81788e0693b33ee84f6a602a2fac965fb22ad2cec20c5f2950d3fa16af80cb18a274119d WHIRLPOOL a3fbc49445969106ae84e931bfe16f7af99e620c026aa2af80881e4b76a3e9c9367919fd974bca8e0ff7c571d36621990f25f517f2cd5bc1945962294d5b9b73 diff --git a/sci-biology/aaindex/aaindex-9.1-r1.ebuild b/sci-biology/aaindex/aaindex-9.1-r1.ebuild new file mode 100644 index 000000000000..068902e96fae --- /dev/null +++ b/sci-biology/aaindex/aaindex-9.1-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Amino acid indices and similarity matrices" +HOMEPAGE="http://www.genome.jp/aaindex/" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="public-domain" +SLOT="0" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emboss minimal" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir AAINDEX || die + einfo + einfo "Indexing AAindex for usage with EMBOSS." + EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die "Indexing AAindex failed" + einfo + fi +} + +src_install() { + dodoc ${PN}.doc + + if ! use minimal; then + insinto /usr/share/${PN} + doins ${PN}{1,2,3} + fi + + if use emboss; then + insinto /usr/share/EMBOSS/data/AAINDEX + doins -r AAINDEX/. + fi +} diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml new file mode 100644 index 000000000000..ffe91c9020d6 --- /dev/null +++ b/sci-biology/aaindex/metadata.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + Amino acid indices and similarity matrices maintained at Kyoto + University. An amino acid index is a set of 20 numerical values + representing any of the different physicochemical and biological + properties of amino acids. The AAindex1 section of the Amino Acid + Index Database is a collection of published indices together with the + result of cluster analysis using the correlation coefficient as the + distance between two indices. This section currently contains 494 + indices. Another important feature of amino acids that can be + represented numerically is the similarity between amino acids. Thus, a + similarity matrix, also called a mutation matrix, is a set of 210 + numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used + for sequence alignments and similarity searches. The AAindex2 section + of the Amino Acid Index Database is a collection of published amino + acid mutation matrices together with the result of cluster analysis. + This section currently contains 83 matrices. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest new file mode 100644 index 000000000000..53cbd51fdb65 --- /dev/null +++ b/sci-biology/abyss/Manifest @@ -0,0 +1,5 @@ +DIST abyss-2.0.2.tar.gz 1036135 SHA256 6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 WHIRLPOOL 23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e +EBUILD abyss-2.0.2-r1.ebuild 1255 SHA256 76cd126c146ca100d00fe6b48b8a9a2bfcdef7db9dabfcb7ab6eccbeaa3d7c68 SHA512 2a75296cc2d5884be09ce2aa6280af3e54735501125da0dea4cbd297f18061a94ac1ced98990087c209f196c8f624b4cae24c7f7c383913b59ba0c51e9823ed9 WHIRLPOOL d50d12d60d22f98d320a42693de9eef945d64067ac0b5cf25cfc24b8b657789b04b8e08c9ab133a3683b0486b8d0441ec35d2c7d24eb1f2930e78ca152d84d2f +MISC ChangeLog 5076 SHA256 033515486551f430c662c0f8f24932c83fbd40ce3dc20fc487aad8b2449d93e3 SHA512 b16c9e47c2af4c8dcdf421f487aa4d665b3658457fc77a19f41bc62b7d12df756f7fd0d5c0ff2e03b0c3dd4558414126be15c0c6e9cff10d06c4e1e45871bb21 WHIRLPOOL 45db002d9a6e585df0460ab09fd046d6dab8cda26a81aba849793ed1d0c54ce13330b7963274d633410934d6f7d6c405a91f145c33239afb6082fe865449288e +MISC ChangeLog-2015 3086 SHA256 3e295bd3a13f20016e1baaf773c888fad647ad1aa09f77719590a3d01b33e320 SHA512 28de3b6bb48d775fb1ecd1bcc37aadf43451a7200ce691b11833a41dcdde6046e70e7a3b76d5fecb2cadcd96fd94d3e67b6ad1758b9132028aac19339c8e9bd4 WHIRLPOOL 9d73031727499d87e932b55833512068e36c57ca6ab4dc06d8a458f3db89fefda263d858d322468f6de5a9a34113f1a826a01878c633d19ed3d79d962ba410ff +MISC metadata.xml 572 SHA256 5649b00a9f038a5916a2205b92cf55df64d886a7451362d2ad481d09dd53f412 SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198 WHIRLPOOL cd121dd5eeb4084400bc72b6c9af38076b064d5f12b19fe7964a592fdd881fd1bafd4cd8a2389d9ba5a03a99762452e2f53d7898916b09e258692d24a23a24c9 diff --git a/sci-biology/abyss/abyss-2.0.2-r1.ebuild b/sci-biology/abyss/abyss-2.0.2-r1.ebuild new file mode 100644 index 000000000000..0d1c14ac265e --- /dev/null +++ b/sci-biology/abyss/abyss-2.0.2-r1.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost:= + misc-haskell? ( + dev-libs/gmp:0= + virtual/libffi:0= + ) + mpi? ( sys-cluster/openmpi )" +DEPEND="${RDEPEND} + misc-haskell? ( + dev-lang/ghc + dev-haskell/mmap + )" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_prepare() { + default + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + # disable building haskell tool Misc/samtobreak + # unless request by user: bug #534412 + use misc-haskell || export ac_cv_prog_ac_ct_GHC= + + econf $(use_enable openmp) +} diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml new file mode 100644 index 000000000000..47116e507d89 --- /dev/null +++ b/sci-biology/abyss/metadata.xml @@ -0,0 +1,18 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>haskell@gentoo.org</email> + <name>Gentoo Haskell</name> + </maintainer> + <use> + <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> + </use> + <upstream> + <remote-id type="github">bcgsc/abyss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest new file mode 100644 index 000000000000..16522ef9827f --- /dev/null +++ b/sci-biology/allpathslg/Manifest @@ -0,0 +1,7 @@ +AUX allpathslg-52488_fix-buildsystem.patch 1301 SHA256 c04a16ed21984ccbed04fa38485ad16fd4de5f33ae0b79bc5a270803d0671486 SHA512 f23495515581947761de8b14580b0c28070f38a9a1c9b91403cdf5fbc0efcf48230a3ef7281f9700f0c45b87ceda97733d9329cfacb6112f60fc2f246a0416b9 WHIRLPOOL 87d51db82e35b88c6195415ade7186bea1439d840c21dd36816a38165706f77d5690bf326001c6ebb59b62021ca6d6e60bbe03a3d96bc50a244992af369bd3d8 +AUX allpathslg-52488_remove-namespace-std.patch 49158 SHA256 7b04780e03591801e8f1ea404604c1dbeddaa304880c1c755c8a594d4d2b55eb SHA512 e3c918519448c0e37ad57bc90fb6eacad246e53cd759fbf910d725358c1d2e2712f1d1008002e751e0c4decae8a37a5f78e0a0d39dd6a276475aa92cc310d509 WHIRLPOOL 3d739564f72b0d6fcbeb10c4188d50ea9f46725c992d96600377186f25d1f20baacccdd3c1b7debf236a6455f7d66980e8aa79e68b28998f216c067fde106727 +DIST allpathslg-52488.tar.gz 3121949 SHA256 035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d WHIRLPOOL c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4 +EBUILD allpathslg-52488-r2.ebuild 1462 SHA256 03dd7434b4ff119c69350a3de3bf444442b33719a4313c00ae622971cc23a605 SHA512 9e2ae363ed6342015b773de5aba2d62ba30321b1e36d7f9f7bb46dc00592e6d9426291e4dc096ca437640466a4966b65c7217f34a6c5df697c43f43fa5d4c0e8 WHIRLPOOL 8cd24d047e67f3820a15f1dec87f145609eadd301fe93679f7b8580f7f10aa7715274e901a1327dde4fac6b2ca87f8d6a823e3f16adf683e16e746125c2c9406 +MISC ChangeLog 4371 SHA256 4529ee3eecccd149e31b1ccd37aa77f6c53bb896931ec4442f5b5ab9f49b8711 SHA512 2069d8500668efaee450cefe842c2b49c50fba619334943f81271dbeb24d2fe29587f0eb29582f8ea4c0aaf456c91245d1ca0f074138696ae72fa6b766bafacb WHIRLPOOL fb10e6e2297eda9f0c1223562805226b3ae235cae36a3cb7e19eff3d788830f7c373f5ad0ad7743f9665466e2ce24c358b3e9c315baa6a02f4e413050eb55d46 +MISC ChangeLog-2015 3047 SHA256 d1965964e6a3587e3ba74badf03f4842fc00bde406aff79932abaf63b8c84788 SHA512 c248db08878f989779bfae72281d76e3fb08e021732ad5ad557d2630ae8e18ffaad30a6b465ffb7f50efea957941554ffc838a959d8de240e49b028653d9f181 WHIRLPOOL c77d8923472edb1f8090897201f2c251c356733d959b6246ddead36ecc8a97fa4f576f3462399428d13dac0111adbb788c76e946b8d3cbccf7a5d3356e175d91 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild new file mode 100644 index 000000000000..e4c4d95288fd --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools flag-o-matic toolchain-funcs + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + !sci-biology/allpaths + !sci-biology/vaal" +DEPEND=" + ${RDEPEND} + dev-libs/boost:=" + +PATCHES=( + "${FILESDIR}/${P}_fix-buildsystem.patch" + "${FILESDIR}/${P}_remove-namespace-std.patch" +) + +pkg_pretend() { + # as of release 44849, GCC 4.7.0 (or higher) is required + # seems pre gcc-4.7 users must stay with: + # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz + if [[ ${MERGE_TYPE} != binary ]]; then + tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \ + die "You need to use gcc >4.7" + fi +} + +pkg_setup() { + if ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi +} + +src_prepare() { + default + + eautoreconf +} diff --git a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch new file mode 100644 index 000000000000..7944eb5469dc --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch @@ -0,0 +1,33 @@ +Fix build system to remove hardcoded debugging flags. + +--- allpathslg-52488/configure.ac ++++ allpathslg-52488/configure.ac +@@ -12,7 +12,7 @@ + AC_OPENMP + AC_OPENMP_CHECK + +-CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG" ++CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG" + + OS_RELEASE="`uname -r`" + AC_SUBST(CXXFLAGS) +--- allpathslg-52488/m4/broad.m4 ++++ allpathslg-52488/m4/broad.m4 +@@ -35,12 +35,14 @@ + OLD_CFLAGS=$CFLAGS + CFLAGS="$OPENMP_CFLAGS $CFLAGS" + AC_MSG_CHECKING([validity of OpenMP configuation.]) +- AC_LINK_IFELSE([#ifndef _OPENMP ++ AC_LINK_IFELSE([ ++ AC_LANG_SOURCE([[ ++ #ifndef _OPENMP + choke me + #endif + #include <omp.h> +- int main () { return omp_get_num_threads (); }], +- [], ++ int main () { return omp_get_num_threads (); } ++ ]])],[], + [AC_MSG_BROAD_FAIL([Your compiler must support OpenMP.])]) + CXXFLAGS=$OLD_CXXFLAGS + CFLAGS=$OLD_CFLAGS diff --git a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch new file mode 100644 index 000000000000..56d04069435c --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch @@ -0,0 +1,1770 @@ +Remove 'using namespace std' causing massive havoc with newly +introduced std::align in GCC-5. Fix bug +https://bugs.gentoo.org/show_bug.cgi?id=568440 + +--- allpathslg-52488/src/agp/AgpFile.cc ++++ allpathslg-52488/src/agp/AgpFile.cc +@@ -4,6 +4,8 @@ + #include "agp/AgpFile.h" + #include "TokenizeString.h" + ++using std::cerr; ++ + char agp_contig::TypeChar_() const + { + switch ( type_ ) +--- allpathslg-52488/src/agp/AgpFile.h ++++ allpathslg-52488/src/agp/AgpFile.h +@@ -9,6 +9,8 @@ + + #include "agp/AgpMods.h" + ++using std::max; ++ + class agp_entry + { + public: +--- allpathslg-52488/src/agp/AgpMods.cc ++++ allpathslg-52488/src/agp/AgpMods.cc +@@ -7,6 +7,8 @@ + + #include "system/System.h" + ++using std::istrstream; ++ + bool + agp_mods::SuperShouldBeRemoved( int super_id ) const + { +--- allpathslg-52488/src/agp/AgpMods.h ++++ allpathslg-52488/src/agp/AgpMods.h +@@ -7,6 +7,8 @@ + #include "String.h" + #include "Vec.h" + ++using std::swap; ++ + // The class contig_range provides begin and end positions on a + // contig. If the end position is before the begin position, the + // range is considered reversed. If a length is provided, the range +--- allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc ++++ allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc +@@ -56,6 +56,8 @@ + #include "feudal/VirtualMasterVec.h" + #include "random/Shuffle.h" + ++using std::map; ++ + typedef VirtualMasterVec<BaseVec> VBaseVecVec; + typedef VirtualMasterVec<QualVec> VQualVecVec; + +--- allpathslg-52488/src/AnAssemblyClass.h ++++ allpathslg-52488/src/AnAssemblyClass.h +@@ -19,6 +19,8 @@ + #include "ReadLocation.h" + #include "ReadPairing.h" + ++using std::map; ++ + class assembly; + + class super { +--- allpathslg-52488/src/efasta/EfastaTools.cc ++++ allpathslg-52488/src/efasta/EfastaTools.cc +@@ -19,6 +19,8 @@ + #include "math/Array.h" + #include <iostream> + ++using std::set; ++ + #define Err(message) \ + { cout << message << endl << "\nInvalid.\n" << endl; \ + TracebackThisProcess( ); } +--- allpathslg-52488/src/Equiv.cc ++++ allpathslg-52488/src/Equiv.cc +@@ -9,6 +9,8 @@ + #include "Equiv.h" + #include "Vec.h" + ++using std::swap; ++ + bool equivalence_relation::equiv(int a, int b) const + { if ( a == b ) return true; + int c = a; +--- allpathslg-52488/src/FastaFilestream.cc ++++ allpathslg-52488/src/FastaFilestream.cc +@@ -13,6 +13,8 @@ + + #include <strstream> + ++using std::string; ++ + template <typename vecT, typename seqT, typename convT, typename verifT> + FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename, + FastaNameParser* name_parser ) +--- allpathslg-52488/src/FastaFilestreamPreview.cc ++++ allpathslg-52488/src/FastaFilestreamPreview.cc +@@ -11,6 +11,8 @@ + + #include <algorithm> + ++using std::streamoff; ++ + FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream) + : max_sequence_size_(0), start_offset_(0) + { +--- allpathslg-52488/src/FastaFilestreamPreview.h ++++ allpathslg-52488/src/FastaFilestreamPreview.h +@@ -12,6 +12,8 @@ + + #include "Vec.h" + ++using std::streampos; ++ + // FastaFilestreamPreview understands just enough about the fasta + // format to be able to count the number of sequences in the specified + // filestream and to know where each sequence starts in that filestream. +--- allpathslg-52488/src/Fastavector.cc ++++ allpathslg-52488/src/Fastavector.cc +@@ -14,6 +14,8 @@ + #include <istream> + #include <string> + ++using std::max; ++ + // Split this into chunks, separated by gaps ('n'), and return each chunk as a + // gapless fastavector. + // TODO: generalize this into a templatized STL algorithm. +--- allpathslg-52488/src/Fastavector.h ++++ allpathslg-52488/src/Fastavector.h +@@ -24,6 +24,9 @@ + #include <iostream> + #include <unistd.h> + ++using std::string; ++using std::istringstream; ++ + typedef std::tuple<String, int, int> FastaRegion; + + class fastaindex { +--- allpathslg-52488/src/FetchReads.cc ++++ allpathslg-52488/src/FetchReads.cc +@@ -36,6 +36,8 @@ + #include "Qualvector.h" + #include "random/Random.h" + ++using std::istringstream; ++ + // Heuristic constants: + + namespace +--- allpathslg-52488/src/feudal/BaseVec.cc ++++ allpathslg-52488/src/feudal/BaseVec.cc +@@ -21,6 +21,7 @@ + using std::ostream; + using std::cout; + using std::endl; ++using std::max_element; + + // Cap: in a given basevector, replace any sequence of N > n identical + // bases by n of the same base. +--- allpathslg-52488/src/graph/Digraph.cc ++++ allpathslg-52488/src/graph/Digraph.cc +@@ -17,6 +17,9 @@ + #include "graph/Digraph.h" + #include "math/Functions.h" + ++using std::make_pair; ++using std::priority_queue; ++ + void digraph::TransferEdges( int v, int w, const Bool enter_only ) + { ForceAssert( v != w ); + +--- allpathslg-52488/src/graph/Digraph.h ++++ allpathslg-52488/src/graph/Digraph.h +@@ -52,6 +52,8 @@ + #include "system/TraceVal.h" + #include <cstddef> + ++using std::function; ++ + typedef pair<int, int> VertexPair; + + typedef int vrtx_t; +--- allpathslg-52488/src/graph/DigraphTemplate.h ++++ allpathslg-52488/src/graph/DigraphTemplate.h +@@ -34,6 +34,8 @@ + #include "graph/Digraph.h" + #include <cstddef> + ++using std::make_pair; ++ + template<class E> vec<int> digraphE<E>:: EdgesBoundedBy( const int e1, const int e2, + const vec<int>& to_left, const vec<int>& to_right ) const + { int v = to_right[e1], w = to_left[e2]; +--- allpathslg-52488/src/graph/GraphAlgorithms.h ++++ allpathslg-52488/src/graph/GraphAlgorithms.h +@@ -9,7 +9,7 @@ + #ifndef GRAPH__GRAPH_ALGORITHMS__H_ + #define GRAPH__GRAPH_ALGORITHMS__H_ + +- ++using std::map; + + // -------------- Union Find --------------- + // +--- allpathslg-52488/src/IndexedAlignmentPlusVector.h ++++ allpathslg-52488/src/IndexedAlignmentPlusVector.h +@@ -15,6 +15,8 @@ + + #include "Alignment.h" + ++using std::streampos; ++using std::streamoff; + + // This class encapsulates the header information for both vectors and indices. + +--- allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h ++++ allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h +@@ -6,6 +6,9 @@ + // Institute is not responsible for its use, misuse, or functionality. // + /////////////////////////////////////////////////////////////////////////////// + ++using std::hex; ++using std::dec; ++ + // --------------------------------- + // NaifTimer + // --------------------------------- +--- allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h ++++ allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h +@@ -13,8 +13,8 @@ + #include "kmers/naif_kmer/LockedBlocks.h" + #include "kmers/naif_kmer/Kmers.h" + +- +- ++using std::make_pair; ++using std::stringstream; + + + +--- allpathslg-52488/src/kmers/naif_kmer/Kmers.h ++++ allpathslg-52488/src/kmers/naif_kmer/Kmers.h +@@ -14,7 +14,7 @@ + + #include "kmers/naif_kmer/KmerFunctions.h" + +- ++using std::string; + + // ---- 256 random 64bit numbers to compute hash key + +--- allpathslg-52488/src/layout/ContigActualloc.h ++++ allpathslg-52488/src/layout/ContigActualloc.h +@@ -17,6 +17,8 @@ + #include "system/Crash.h" + #include "Misc.h" + ++using std::set; ++using std::map; + + // + // Class contig_actualloc +--- allpathslg-52488/src/lookup/ImperfectLookup.h ++++ allpathslg-52488/src/lookup/ImperfectLookup.h +@@ -51,6 +51,8 @@ + #include "lookup/LookupTools.h" + #include "lookup/AlignCollector.h" + ++using std::auto_ptr; ++ + class TaskTimer; + + +--- allpathslg-52488/src/lookup/LookAlign.cc ++++ allpathslg-52488/src/lookup/LookAlign.cc +@@ -29,6 +29,8 @@ + #include "random/Random.h" + #include "system/ParsedArgs.h" + ++using std::istrstream; ++ + String QUERY("QUERY"); + + void look_align::ResetFromAlign(const align & al, const basevector & b1, +--- allpathslg-52488/src/lookup/LookupTable.h ++++ allpathslg-52488/src/lookup/LookupTable.h +@@ -18,6 +18,8 @@ + + #include <set> + ++using std::set; ++ + typedef pair<unsigned int, unsigned int> LocSeq; + + /// +--- allpathslg-52488/src/lookup/QueryLookupTableCore.cc ++++ allpathslg-52488/src/lookup/QueryLookupTableCore.cc +@@ -465,6 +465,9 @@ + #include "system/ParsedArgs.h" + #include "system/file/FileReader.h" + ++using std::istrstream; ++using std::less_equal; ++ + #define ABORT(MSG) \ + { out << MSG << " Abort." << endl << endl; \ + exit(1); } +--- allpathslg-52488/src/lookup/ShortQueryLookup.cc ++++ allpathslg-52488/src/lookup/ShortQueryLookup.cc +@@ -32,6 +32,8 @@ + #include "lookup/AlignCollector.h" + #include "lookup/ImperfectLookup.h" + ++using std::ios_base; ++ + // Run an alignment processing chain: seqs -> look -> receiver -> aligns + // That is, look turns seqs into hits, which receiver accepts + // and turns into alignments which are passed to aligns. The +--- allpathslg-52488/src/Map.h ++++ allpathslg-52488/src/Map.h +@@ -23,7 +23,7 @@ + #include <unordered_map> + #include <ext/hash_map> + using namespace __gnu_cxx; +- ++using std::map; + + template <class K, class V, class C=std::less<K>> + using StdMap = std::map<K,V,C,typename DefaultAllocator<std::pair<K const,V>>::type>; +--- allpathslg-52488/src/math/Array.h ++++ allpathslg-52488/src/math/Array.h +@@ -13,6 +13,8 @@ + #include "Vec.h" + #include "Map.h" + ++using std::fill; ++ + // ============================================================================== + // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> > + // The elements are uninitialized. +--- allpathslg-52488/src/math/Functions.cc ++++ allpathslg-52488/src/math/Functions.cc +@@ -10,7 +10,7 @@ + #include "STLExtensions.h" + #include "math/Functions.h" + +- ++using std::make_pair; + + + /* CombineNormalDistribution Filipe Ribeiro 2009-06-22 +--- allpathslg-52488/src/math/Functions.h ++++ allpathslg-52488/src/math/Functions.h +@@ -15,6 +15,10 @@ + #include <cmath> + #include <numeric> + ++using std::min; ++using std::cerr; ++using std::swap; ++ + // =========================================================================== + // + // Min functions +--- allpathslg-52488/src/math/HoInterval.cc ++++ allpathslg-52488/src/math/HoInterval.cc +@@ -10,6 +10,8 @@ + #include "math/HoInterval.h" + #include "STLExtensions.h" + ++using std::make_pair; ++ + bool ho_interval::Merge(const ho_interval & o) { + if (!Meets(*this,o)) return false; + *this = Span(*this, o); +--- allpathslg-52488/src/math/HoInterval.h ++++ allpathslg-52488/src/math/HoInterval.h +@@ -14,6 +14,8 @@ + #include "feudal/MasterVec.h" + #include "feudal/SerfVec.h" + ++using std::max; ++ + /// Class: ho_interval + /// A half-open interval [a, b). + class ho_interval { +--- allpathslg-52488/src/math/IntFunction.h ++++ allpathslg-52488/src/math/IntFunction.h +@@ -21,6 +21,8 @@ + + #include "MainTools.h" + ++using std::deque; ++using std::fixed; + + #define __INT_FUNCTION_BINARY_VERSION__ 2 + +--- allpathslg-52488/src/PackAlign.h ++++ allpathslg-52488/src/PackAlign.h +@@ -133,6 +133,8 @@ + #include "pairwise_aligners/Mutmer.h" + #include "feudal/BinaryStream.h" + ++using std::make_pair; ++ + const int Bits2 = 3, Bits3 = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, + Bits16 = 65535; + +--- allpathslg-52488/src/PairsManager.h ++++ allpathslg-52488/src/PairsManager.h +@@ -61,6 +61,7 @@ + #include "feudal/BinaryStream.h" + #include <cstddef> + ++using std::make_pair; + + class PairsManager; // forward declaration + +--- allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc ++++ allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc +@@ -19,6 +19,9 @@ + #include "pairwise_aligners/AlignFromMutmers.h" + #include "pairwise_aligners/SmithWatBandedA.h" + ++using std::map; ++using std::set; ++ + // If there's a perfect match of length at least perf but we produced no proper + // alignment, use banded Smith-Waterman to create one. + +--- allpathslg-52488/src/pairwise_aligners/MatchList.cc ++++ allpathslg-52488/src/pairwise_aligners/MatchList.cc +@@ -9,6 +9,8 @@ + + #include "pairwise_aligners/MatchList.h" + ++using std::max; ++ + bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const + { + const vec<Match>& sortedMatches = m_sortedMatches[id1]; +--- allpathslg-52488/src/paths/AlignHyperKmerPath.cc ++++ allpathslg-52488/src/paths/AlignHyperKmerPath.cc +@@ -23,6 +23,9 @@ + #include "paths/KmerBaseBroker.h" + #include "paths/KmerPath.h" + ++using std::ostringstream; ++using std::set; ++ + // Function: AlignHyperKmerPath + // + // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed +--- allpathslg-52488/src/paths/CAltFasta.cc ++++ allpathslg-52488/src/paths/CAltFasta.cc +@@ -11,7 +11,7 @@ + #include "paths/FixSomeIndelsUtils.h" + #include "efasta/EfastaTools.h" + +- ++using std::set; + + /** + * CAltFasta +--- allpathslg-52488/src/paths/ChangeLibraryStats.cc ++++ allpathslg-52488/src/paths/ChangeLibraryStats.cc +@@ -47,8 +47,10 @@ + + int libID = pairs.libraryID( libName ); + ForceAssertLt( libID, nLibraries); ForceAssertGe( libID, 0 ); +- cout << "old: " << PRINT4( libName, libID, pairs.getLibrarySep(libID), pairs.getLibrarySD(libID) ); +- cout << "new: " << PRINT4( libName, libID, sep, dev ); ++ cout << "old: "; ++ PRINT4( libName, libID, pairs.getLibrarySep(libID), pairs.getLibrarySD(libID) ); ++ cout << "new: "; ++ PRINT4( libName, libID, sep, dev ); + pairs.changeLibrarySepSd( libID, sep, dev ); + } + in.close(); +--- allpathslg-52488/src/paths/CorrectLongReadsTools.h ++++ allpathslg-52488/src/paths/CorrectLongReadsTools.h +@@ -16,6 +16,8 @@ + #include "paths/LongReadTools.h" + #include "paths/Uniseq.h" + ++using std::map; ++ + class heuristics { + + public: +--- allpathslg-52488/src/paths/ExtendUnipathSeqs.cc ++++ allpathslg-52488/src/paths/ExtendUnipathSeqs.cc +@@ -13,6 +13,9 @@ + + #include <set> + ++using std::set; ++using std::back_inserter; ++ + void ExtendUnipathSeqs( const vecKmerPath& unipaths, + const vecUnipathSeq& unipathSeqs, + vecUnipathSeq& extendedUnipathSeqs, +--- allpathslg-52488/src/paths/FindErrorsCore.cc ++++ allpathslg-52488/src/paths/FindErrorsCore.cc +@@ -20,6 +20,8 @@ + #include "kmers/naif_kmer/KernelPreCorrector.h" + #include "system/WorklistN.h" + ++using std::map; ++ + static inline + String Tag(String S = "FEC") { return Date() + " (" + S + "): "; } + +--- allpathslg-52488/src/paths/FindErrorsCore.h ++++ allpathslg-52488/src/paths/FindErrorsCore.h +@@ -14,7 +14,7 @@ + + #include "kmers/KmerSpectra.h" + +- ++using std::set; + + class PC_Params + { +--- allpathslg-52488/src/paths/FindUnipathSeedsLG.cc ++++ allpathslg-52488/src/paths/FindUnipathSeedsLG.cc +@@ -16,6 +16,8 @@ + #include "paths/simulation/Placement.h" + #include <thread> + ++using std::ostringstream; ++ + // A whole bunch of variables that are shared by parallel threads. + + static const digraphE<fsepdev>* FG_ptr; +--- allpathslg-52488/src/paths/FindUnipathSeedsLG.h ++++ allpathslg-52488/src/paths/FindUnipathSeedsLG.h +@@ -19,7 +19,7 @@ + #include "paths/simulation/Placement.h" // placement + #include "paths/UnipathNhoodLG.h" // sepdev, fsepdev + +- ++using std::string; + + enum SeedStatus + { SEED_GOOD, SEED_ISOLATED, SEED_SHORT, SEED_HIGH_CN, SEED_ZERO_CN, SEED_RC_ON_REF, SEED_REDUNDANT, SEED_RC_OF_SEED }; +--- allpathslg-52488/src/paths/FixLocal.cc ++++ allpathslg-52488/src/paths/FixLocal.cc +@@ -88,6 +88,8 @@ + #include "paths/Unipath.h" + #include "paths/FindErrorsCore.h" + ++using std::ostringstream; ++ + void AddToPileup( const read_loc& rl, const basevector& b, const qualvector& q, + const basevector& tig, vec<dumbcall>& calls ) + { align a; +--- allpathslg-52488/src/paths/FragmentFillerDefs.h ++++ allpathslg-52488/src/paths/FragmentFillerDefs.h +@@ -28,6 +28,8 @@ + #include <set> + #include <time.h> + ++using std::map; ++ + namespace + { + +--- allpathslg-52488/src/paths/GetHomes.cc ++++ allpathslg-52488/src/paths/GetHomes.cc +@@ -17,6 +17,8 @@ + #include "paths/Uniseq.h" + #include "util/SearchFastb2Core.h" + ++using std::ostringstream; ++ + class vepath { + + public: +--- allpathslg-52488/src/paths/HyperFastavector.cc ++++ allpathslg-52488/src/paths/HyperFastavector.cc +@@ -14,6 +14,8 @@ + #include "feudal/BinaryStream.h" + #include <thread> + ++using std::ostringstream; ++ + // Order a pair of vec<int>s lexicographically using subset relation. + + struct order_vecint_binsubset_pair +--- allpathslg-52488/src/paths/HyperKmerPathCleaner.cc ++++ allpathslg-52488/src/paths/HyperKmerPathCleaner.cc +@@ -11,6 +11,7 @@ + #include "paths/HyperKmerPathCleaner.h" + #include <set> + ++using std::set; + + void HyperKmerPathCleaner::CleanUpGraph( HyperKmerPath& ans ) const { + +--- allpathslg-52488/src/paths/InsertWalker.h ++++ allpathslg-52488/src/paths/InsertWalker.h +@@ -34,7 +34,7 @@ + #include "paths/KmerPath.h" + #include "TaskTimer.h" // TaskTimer + +- ++using std::set; + + + +--- allpathslg-52488/src/paths/InternalMergeImpl.cc ++++ allpathslg-52488/src/paths/InternalMergeImpl.cc +@@ -17,7 +17,7 @@ + #include "paths/InternalMergeImpl.h" + #include "graph/Digraph.h" + +- ++using std::set; + + + /******************************************************************************* +--- allpathslg-52488/src/paths/KmerAlignSet.h ++++ allpathslg-52488/src/paths/KmerAlignSet.h +@@ -12,6 +12,8 @@ + #include "Basevector.h" + #include "CoreTools.h" + ++using std::make_pair; ++ + // KmerAlignSet. It represents a set of alignments of a read to unibases, although + // in principle the 'read' could be any sequence and the 'unibases' could be any set + // of sequences. +--- allpathslg-52488/src/paths/KmerBaseBroker.h ++++ allpathslg-52488/src/paths/KmerBaseBroker.h +@@ -20,6 +20,8 @@ + #include <algorithm> // for set_union + #include <map> + ++using std::map; ++ + /** + Class: KmerBaseBrokerTemplate + +--- allpathslg-52488/src/paths/KmerPathDatabase.cc ++++ allpathslg-52488/src/paths/KmerPathDatabase.cc +@@ -4,6 +4,8 @@ + #include "feudal/BinaryStream.h" + #include <map> + ++using std::map; ++ + // Methods of class KmerPathDatabaseTemplate. + + template <class TAG> +--- allpathslg-52488/src/paths/KmerPath.h ++++ allpathslg-52488/src/paths/KmerPath.h +@@ -22,6 +22,8 @@ + #include "HashSimple.h" + #include "graph/Digraph.h" + ++using std::make_pair; ++ + class KmerPathLoc; // forward declaration + + /** +--- allpathslg-52488/src/paths/KmerPathInterval.cc ++++ allpathslg-52488/src/paths/KmerPathInterval.cc +@@ -128,11 +128,11 @@ + } + + template void Contains( const vec<tagged_rpint>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append, int cap ); ++ vec<longlong>& answer, bool append = false, int cap = -1 ); + template void Contains( const vec<big_tagged_rpint>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append, int cap ); ++ vec<longlong>& answer, bool append = false, int cap = -1 ); + template void Contains( const vec<new_tagged_rpint>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append, int cap ); ++ vec<longlong>& answer, bool append = false, int cap = -1 ); + + // Overload Contains() with a second version that looks for all intervals overlapping + // a given KmerPathInterval, instead of a single kmer. +@@ -203,11 +203,11 @@ + } + + template void Contains( const vec<tagged_rpint>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append, int cap ); ++ vec<longlong>& answer, bool append = false, int cap = -1 ); + template void Contains( const vec<big_tagged_rpint>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append, int cap ); ++ vec<longlong>& answer, bool append = false, int cap = -1 ); + template void Contains( const vec<new_tagged_rpint>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append, int cap ); ++ vec<longlong>& answer, bool append = false, int cap = -1 ); + + // This will efficiently find a single instance of the requested kmer. + // Intended for base lookup, where you don't need to find all of them. +--- allpathslg-52488/src/paths/KmerPathInterval.h ++++ allpathslg-52488/src/paths/KmerPathInterval.h +@@ -8,6 +8,8 @@ + #include "CommonSemanticTypes.h" + #include "feudal/BinaryStreamTraits.h" + ++using std::max; ++ + // Portability note: endianness + // The implementations here would need to be changed for big endian architectures. + +@@ -116,6 +118,15 @@ + To do: check that "gaps in kmer paths are not used for assembly from short reads" + is true. + */ ++ ++class KmerPathInterval; ++ ++template<class TAG> ++void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 ); ++ ++template<class TAG> ++void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 ); ++ + class KmerPathInterval { + public: + KmerPathInterval( ) { } +@@ -364,11 +375,11 @@ + + template<class TAG> + friend void Contains( const vec<TAG>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); +@@ -491,11 +502,11 @@ + + template<class TAG> + friend void Contains( const vec<TAG>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); +@@ -622,11 +633,11 @@ + + template<class TAG> + friend void Contains( const vec<TAG>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k ); +--- allpathslg-52488/src/paths/KPatch.cc ++++ allpathslg-52488/src/paths/KPatch.cc +@@ -32,6 +32,8 @@ + #include "paths/AssemblyEdit.h" + #include "paths/GetNexts.h" + ++using std::ostringstream; ++ + template<int K> void PatchMe( const vec<basevector>& jbases_sorted, + const vec<int64_t>& jbases_sorted_id, const PairsManager& jpairs, + const vec< triple<int64_t,int,int> >& jaligns, const vec<superb>& scaffolds, +--- allpathslg-52488/src/paths/LinkingPairs.cc ++++ allpathslg-52488/src/paths/LinkingPairs.cc +@@ -9,6 +9,8 @@ + #include "paths/LinkingPairs.h" + #include "math/Array.h" + ++using std::multiset; ++ + void LinkingPairs::Init(int nlibs_, const vec<int>& lens ) + { + nlibs = nlibs_; +--- allpathslg-52488/src/paths/long/EvalByReads.cc ++++ allpathslg-52488/src/paths/long/EvalByReads.cc +@@ -19,6 +19,8 @@ + #include <queue> + #include <omp.h> + ++using std::priority_queue; ++ + namespace { + struct CompareReadPlaceByQsum { + bool operator() (const read_place& a, const read_place& b) +--- allpathslg-52488/src/paths/long/EvalCorrected.cc ++++ allpathslg-52488/src/paths/long/EvalCorrected.cc +@@ -25,6 +25,8 @@ + #include "paths/long/MakeKmerStuff.h" + #include "random/Random.h" + ++using std::set; ++ + void EvalCorrected( + const VecEFasta& corrected0, // corrected reads + const vec<int>& cid, // ids of corrected reads +--- allpathslg-52488/src/paths/long/fosmid/Fosmids.cc ++++ allpathslg-52488/src/paths/long/fosmid/Fosmids.cc +@@ -15,6 +15,9 @@ + #include "paths/long/fosmid/Fosmids.h" + #include "math/HoInterval.h" + ++using std::istringstream; ++using std::ostringstream; ++ + vec<int> ChrSizes(void) + { + return {249250621,243199373,198022430,191154276,180915260,171115067, +--- allpathslg-52488/src/paths/long/KmerAlign.cc ++++ allpathslg-52488/src/paths/long/KmerAlign.cc +@@ -12,6 +12,8 @@ + #include "Equiv.h" + #include "VecUtilities.h" + ++using std::map; ++ + void KmerAlign( + const vec< pair<int,int> > & offset, + vec< pair<int,int> > & aligns, +--- allpathslg-52488/src/paths/long/OverlapReads.cc ++++ allpathslg-52488/src/paths/long/OverlapReads.cc +@@ -10,6 +10,10 @@ + #include "FeudalMimic.h" + #include <queue> + ++using std::max; ++using std::queue; ++using std::make_pair; ++ + // ================================ static methods ============================= + + // If tail b1[len1-overlap:len1) is the same as head b2[0: overlap) +--- allpathslg-52488/src/paths/long/RefTraceTools.cc ++++ allpathslg-52488/src/paths/long/RefTraceTools.cc +@@ -10,6 +10,8 @@ + #include "VecUtilities.h" + #include "math/HoInterval.h" + ++using std::get; ++ + void CreateHBPlus(const HyperBasevector& hb, const vec<int>& inv, + HyperBasevector& hbp, vec<pair<int,Bool>>& hbp_to_hb) + { +--- allpathslg-52488/src/paths/long/ultra/ConsensusScoreModel.cc ++++ allpathslg-52488/src/paths/long/ultra/ConsensusScoreModel.cc +@@ -12,6 +12,8 @@ + #include "VecUtilities.h" + #include <map> + ++using std::map; ++ + ConsensusScoreModel::ConsensusScoreModel( double del_rate, double ins_rate, double sub_rate, + bool ignore_matching_score, bool score_fast ) + { +--- allpathslg-52488/src/paths/long/VariantCallTools.cc ++++ allpathslg-52488/src/paths/long/VariantCallTools.cc +@@ -27,6 +27,8 @@ + #include "paths/long/VariantReadSupport.h" + #include "kmers/KMer.h" + ++using std::stack; ++ + namespace { + + bool IsBubbleEdge(int eid, const HyperBasevector& hb, const vec<int>& to_left, +--- allpathslg-52488/src/paths/long/VariantReadSupport.cc ++++ allpathslg-52488/src/paths/long/VariantReadSupport.cc +@@ -23,6 +23,13 @@ + #include "paths/long/ReadOriginTracker.h" + #include "paths/long/EvalByReads.h" + ++#include <cmath> ++ ++using std::get; ++using std::make_tuple; ++using std::ignore; ++using std::tie; ++ + namespace { + void CalcLengthProbSimple(vec<double>&vOut,const double dProbIns_len, const double dProbDel_len, const uint64_t org_length){ + const double dProbIns=dProbIns_len; +@@ -158,7 +165,7 @@ + for(uint64_t ff=1;ff<nFlavors;++ff){ + for( size_t ll = 2 ; ll <= get<0>(n_q_len[ff]) ; ++ll){ dFactor /= (long double)(ll); } + } +- if( dFactor==std::numeric_limits<long double>::infinity() || isnan(dFactor) ){ dFactor=1.0; } ++ if( dFactor==std::numeric_limits<long double>::infinity() || std::isnan(dFactor) ){ dFactor=1.0; } + if(verbosity>0) std::cout << "dFactor " << dFactor << std::endl; + + long double dDenom=0.0; +@@ -193,7 +200,7 @@ + } + } + if(verbosity>0) std::cout <<"denom: " << dDenom<< std::endl; +- if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || isnan(dDenom)) return; ++ if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || std::isnan(dDenom)) return; + ForceAssert(dDenom>0); + if(verbosity>0){ + for( uint64_t row=0;row<nFlavors;++row){ +--- allpathslg-52488/src/paths/long/VariantReadSupport.h ++++ allpathslg-52488/src/paths/long/VariantReadSupport.h +@@ -5,6 +5,8 @@ + #include "Qualvector.h" + #include "paths/HyperBasevector.h" + ++using std::tuple; ++ + // forward declaration + class read_place; + class ReadOriginTracker; +--- allpathslg-52488/src/paths/long/Variants.cc ++++ allpathslg-52488/src/paths/long/Variants.cc +@@ -22,6 +22,8 @@ + #include "paths/long/VariantFilters.h" + #include "paths/long/VariantPostProcess.h" + ++using std::set; ++ + int MarkVariants( HyperEfasta& he, const vec<VariantSignature>& v_signatures, + const long_logging& logc ) + { double clock = WallClockTime( ); +--- allpathslg-52488/src/paths/LongReadTools.h ++++ allpathslg-52488/src/paths/LongReadTools.h +@@ -17,6 +17,8 @@ + #include "kmers/KmerRecord.h" + #include "paths/AssemblyEdit.h" + ++using std::ostringstream; ++ + // A gap patcher is defined by left and right ints u1 and u2, and a BaseVec r, + // whose left end aligns to u1 starting at tpos1 and whose right end aligns to u2 + // ending at tpos2, where the positions are in terms of the BaseVecs associated +--- allpathslg-52488/src/paths/MakeScaffoldsCloseBest.cc ++++ allpathslg-52488/src/paths/MakeScaffoldsCloseBest.cc +@@ -29,6 +29,8 @@ + #include "paths/reporting/CLinkBundle.h" + #include <sstream> + ++using std::ostringstream; ++ + // An slink is a link between scaffolds. The first scaffold is not represented + // in the object. + +--- allpathslg-52488/src/paths/Mixmer.cc ++++ allpathslg-52488/src/paths/Mixmer.cc +@@ -73,6 +73,9 @@ + #include "util/ReadTracker.h" + #include "util/SearchFastb2Core.h" + ++using std::ostringstream; ++using std::istrstream; ++ + // CorrectErrors. + + void CorrectErrors( vecbasevector& bases, vecqualvector& quals, +--- allpathslg-52488/src/paths/MuxGraph.cc ++++ allpathslg-52488/src/paths/MuxGraph.cc +@@ -6,6 +6,7 @@ + + #include <set> + ++using std::set; + + // Functions to translate pathIds to nodeIds and back. + +--- allpathslg-52488/src/paths/MuxSearchAgent.h ++++ allpathslg-52488/src/paths/MuxSearchAgent.h +@@ -15,6 +15,10 @@ + #include "paths/MuxSearchState.h" + #include "paths/MuxSearchPolicy.h" + ++using std::hex; ++using std::dec; ++using std::mem_fun; ++ + /// The search agent directed by the SearchDirector of a + /// KmerPathMuxSearcher. + /// +--- allpathslg-52488/src/paths/MuxSearchPolicy.h ++++ allpathslg-52488/src/paths/MuxSearchPolicy.h +@@ -29,6 +29,7 @@ + #include <hash_set> + #endif + ++using std::map; + + //////////////////////////////////////////////////////////////////////////// + /// +--- allpathslg-52488/src/paths/OffsetTracker.cc ++++ allpathslg-52488/src/paths/OffsetTracker.cc +@@ -10,6 +10,8 @@ + #include "paths/OffsetTracker.h" + #include <queue> + ++using std::priority_queue; ++ + MutableOffsetTracker::MutableOffsetTracker( const vecUnipathSeq& unipathSeqs, + const MuxGraph& inverseMuxGraph, + const int firstSuperSeq, +--- allpathslg-52488/src/paths/PairDistFitting.h ++++ allpathslg-52488/src/paths/PairDistFitting.h +@@ -38,7 +38,7 @@ + // + template <class T> + void MostProbableGap( const T& distr, const int len1, const int len2, const vec< pair< int, int > >& links, +- int& gap, int& std, bool verbose=false ) ++ int& gap, int& std, bool verbose ) + { + ForceAssertGt( links.isize(), 0 ); + // find the averge of x1 + x2 ( <x1+x2> = <L> - g in the ideal case ) +--- allpathslg-52488/src/paths/PairDistModels.h ++++ allpathslg-52488/src/paths/PairDistModels.h +@@ -23,6 +23,8 @@ + #include <map> + #include "math/IntDistribution.h" + ++using std::map; ++ + // ===================================================== + // Class ProbFuncInterface + // +--- allpathslg-52488/src/paths/PatcherCottageCore.cc ++++ allpathslg-52488/src/paths/PatcherCottageCore.cc +@@ -22,6 +22,8 @@ + #include "system/AllOfOutput.h" + #include "system/SharedMem.h" + ++using std::ostringstream; ++ + void PatcherCottageCore( basevector L, basevector R, const int sep, + const int dev, vecbasevector& reads, vecqualvector& quals, + vec< pair<int,int> >& pairs, String& report, +--- allpathslg-52488/src/paths/PolymorphismRemoveCore.h ++++ allpathslg-52488/src/paths/PolymorphismRemoveCore.h +@@ -19,7 +19,7 @@ + + #include "kmers/naif_kmer/KmerFreqAffixesMap.h" + +- ++using std::map; + + typedef Kmer29 Kmer_t; + typedef KmerFreqAffixes<Kmer_t> KmerRec_t; +--- allpathslg-52488/src/paths/ReadsToPathsCoreX.cc ++++ allpathslg-52488/src/paths/ReadsToPathsCoreX.cc +@@ -20,6 +20,8 @@ + #include "paths/MakeAlignsPathsParallelX.h" + #include "paths/ReadsToPathsCoreX.h" + ++using std::map; ++ + static inline + String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } + +--- allpathslg-52488/src/paths/RemodelGapTools.cc ++++ allpathslg-52488/src/paths/RemodelGapTools.cc +@@ -18,6 +18,9 @@ + #include "paths/RemodelGapTools.h" + #include "random/NormalDistribution.h" + ++using std::istringstream; ++using std::ostringstream; ++ + // GapComp + // + // d = possible gap +--- allpathslg-52488/src/paths/reporting/CLinkBundle.cc ++++ allpathslg-52488/src/paths/reporting/CLinkBundle.cc +@@ -8,6 +8,8 @@ + + #include "paths/reporting/CLinkBundle.h" + ++using std::make_pair; ++ + /** + * CLinkBundle + * Constructor +--- allpathslg-52488/src/paths/reporting/CSuperLinks.cc ++++ allpathslg-52488/src/paths/reporting/CSuperLinks.cc +@@ -15,6 +15,8 @@ + #include "paths/reporting/COffset.h" + #include "paths/reporting/CSuperLinks.h" + ++using std::set; ++ + /** + * class CSuperLinks + * Constructor +--- allpathslg-52488/src/paths/reporting/MapSeeds.cc ++++ allpathslg-52488/src/paths/reporting/MapSeeds.cc +@@ -24,7 +24,7 @@ + #include "paths/simulation/Placement.h" + #include "feudal/BinaryStream.h" + +- ++using std::ostringstream; + + // MakeDepend: dependency QueryLookupTable + +--- allpathslg-52488/src/paths/SamplePairedReadDistributions.cc ++++ allpathslg-52488/src/paths/SamplePairedReadDistributions.cc +@@ -68,6 +68,8 @@ + #include "math/IntDistribution.h" + #include "math/IntFrequencies.h" + ++using std::list; ++ + static inline + String Tag(String S = "SPRD") { return Date() + " (" + S + "): "; } + +--- allpathslg-52488/src/paths/SamplePairedReadStats.cc ++++ allpathslg-52488/src/paths/SamplePairedReadStats.cc +@@ -46,6 +46,8 @@ + #include "paths/HyperBasevector.h" + #include "paths/ReadsToPathsCoreX.h" + ++using std::list; ++ + // auxiliary routines ------------------------------- + void pair_alignment_data( const PairsManager& pairs, const vecbasevector& reads, const VecQualNibbleVec &quals, + FirstLookupFinderECJ& lfinder, FirstLookupFilterECJ& lfilter, +--- allpathslg-52488/src/paths/SimpleGapCloser.cc ++++ allpathslg-52488/src/paths/SimpleGapCloser.cc +@@ -44,6 +44,8 @@ + #include "paths/Unipath.h" + #include "system/AllOfOutput.h" + ++using std::ostringstream; ++ + class bridge { + + public: +--- allpathslg-52488/src/paths/SimpleWalk.cc ++++ allpathslg-52488/src/paths/SimpleWalk.cc +@@ -15,6 +15,9 @@ + #include "paths/PairedPair.h" + #include "paths/SimpleWalk.h" + ++using std::make_pair; ++using std::priority_queue; ++ + namespace + { + +--- allpathslg-52488/src/paths/simulation/VCF.cc ++++ allpathslg-52488/src/paths/simulation/VCF.cc +@@ -16,6 +16,8 @@ + #include "system/Assert.h" + #include <utility> + ++using std::istringstream; ++ + namespace { + + // split - tokenize a string based on a separator and return a vector of strings representing the +--- allpathslg-52488/src/paths/simulation/VCF.h ++++ allpathslg-52488/src/paths/simulation/VCF.h +@@ -21,7 +21,8 @@ + + using std::string; + using std::vector; +- ++using std::ostringstream; ++using std::map; + + // VCFWriter use a streamlined data structure compared to VCF, which was hard coded to use VCFChromosome + class VCFWriter +--- allpathslg-52488/src/paths/SubmissionPrep.cc ++++ allpathslg-52488/src/paths/SubmissionPrep.cc +@@ -21,6 +21,8 @@ + #include "paths/AssemblyCleanupTools.h" + #include "math/HoInterval.h" + ++using std::ostringstream; ++ + /** + * SubmissionPrep + * +--- allpathslg-52488/src/paths/SubsumptionList.cc ++++ allpathslg-52488/src/paths/SubsumptionList.cc +@@ -2,6 +2,8 @@ + + #include "paths/SubsumptionList.h" + ++using std::back_inserter; ++ + // Functions to translate pathIds to indexes and back. + + OrientedKmerPathId PathIdFromIndex( int index ) +--- allpathslg-52488/src/paths/SuperBaseVector.h ++++ allpathslg-52488/src/paths/SuperBaseVector.h +@@ -10,6 +10,8 @@ + #include <numeric> + #include <functional> + ++using std::mem_fun_ref; ++ + /// A simple class which holds a series of basevectors with + /// (possibly negative) gaps between them. This is what a + /// KmerPath logically maps to in sequence space. The function +--- allpathslg-52488/src/paths/UnibaseCopyNumber3.cc ++++ allpathslg-52488/src/paths/UnibaseCopyNumber3.cc +@@ -43,7 +43,7 @@ + #include <omp.h> + // MakeDepend: library OMP + +- ++using std::istrstream; + + // Check if the gap size from u1 to u2 is the same as from u2* to u1*. + void CheckGaps( +--- allpathslg-52488/src/paths/UnipathEval.cc ++++ allpathslg-52488/src/paths/UnipathEval.cc +@@ -35,6 +35,9 @@ + #include <omp.h> + // MakeDepend: library OMP + ++using std::ostringstream; ++using std::list; ++ + typedef double gc_t; + typedef int unipath_size_t; + typedef BinsVec2 < unipath_size_t, gc_t, PredictionStats > bin2PredStat; +--- allpathslg-52488/src/paths/UnipathFixerTools.cc ++++ allpathslg-52488/src/paths/UnipathFixerTools.cc +@@ -33,6 +33,8 @@ + #include "util/SearchFastb2Core.h" + #include <vector> + ++using std::ostringstream; ++ + size_t const PCottageJoinData::HEADER; + + void AlignReadsToUnipaths( const String& run_dir, const String& jump_reads, +--- allpathslg-52488/src/paths/UnipathNhoodCommon.cc ++++ allpathslg-52488/src/paths/UnipathNhoodCommon.cc +@@ -12,6 +12,8 @@ + #include "paths/simulation/Placement.h" + #include <sstream> + ++using std::ostringstream; ++ + /** + Function: PrintNhood + +--- allpathslg-52488/src/paths/UnipathPatcher.cc ++++ allpathslg-52488/src/paths/UnipathPatcher.cc +@@ -47,6 +47,8 @@ + #include "paths/UnipathFixerTools.h" + #include "system/SharedMem.h" + ++using std::istrstream; ++ + void GapStatsAlt( vec<int> gap, vec<int> gapdev, int& gap_ave, int& gapdev_ave ) + { + // If there are less than six gaps, we directly compute their mean. +--- allpathslg-52488/src/paths/Uniseq.cc ++++ allpathslg-52488/src/paths/Uniseq.cc +@@ -498,7 +498,7 @@ + const gapster& gx = G( ).EdgeObjectByIndexFrom( x, 0 ); + uniseq p = Vert(x); + int y = From(x)[0]; +- if ( !To(y).size( ) == 2 ) continue; ++ if ( !(To(y).size( ) == 2) ) continue; + int e = -1; + for ( int j = 0; j < To(y).isize( ); j++ ) + if ( To(y)[j] != x ) e = j; +@@ -518,7 +518,7 @@ + const gapster& gx = G( ).EdgeObjectByIndexTo( x, 0 ); + uniseq p = Vert(x); + int y = To(x)[0]; +- if ( !From(y).size( ) == 2 ) continue; ++ if ( !(From(y).size( ) == 2) ) continue; + int e = -1; + for ( int j = 0; j < From(y).isize( ); j++ ) + if ( From(y)[j] != x ) e = j; +--- allpathslg-52488/src/paths/Useq.cc ++++ allpathslg-52488/src/paths/Useq.cc +@@ -10,6 +10,8 @@ + #include "CoreTools.h" + #include "paths/Useq.h" + ++using std::make_pair; ++ + int useq::Kmers( ) const + { Assert( unibases_ != 0 ); + int kmers = 0; +--- allpathslg-52488/src/PrintAlignment.h ++++ allpathslg-52488/src/PrintAlignment.h +@@ -14,6 +14,8 @@ + #include "CoreTools.h" + #include "Qualvector.h" + ++using std::ostringstream; ++ + void PrintBlanks( ostream& out, int n ); + + template<class BASEVEC> +--- allpathslg-52488/src/Qualvector.cc ++++ allpathslg-52488/src/Qualvector.cc +@@ -10,6 +10,8 @@ + #include "FastIfstream.h" + #include "Qualvector.h" + ++using std::istrstream; ++ + /// \file + /// \ingroup grp_quals + /// \copydoc Qualvector.h +--- allpathslg-52488/src/ReadLocation.cc ++++ allpathslg-52488/src/ReadLocation.cc +@@ -16,6 +16,9 @@ + #include "Vec.h" + #include "system/file/FileReader.h" + ++using std::streampos; ++using std::map; ++ + void read_location::ForceInBounds( ostream * out_ptr ) + { if ( (int) LengthOfRead( ) > LengthOfContig( ) ) + { if ( out_ptr ) +--- allpathslg-52488/src/ReadLocationUtil.cc ++++ allpathslg-52488/src/ReadLocationUtil.cc +@@ -9,7 +9,7 @@ + #include "STLExtensions.h" + #include "VecAlignmentPlus.h" + +- ++using std::map; + + int AlignsCount( const vec<read_location> &locs, + int loc_id, +--- allpathslg-52488/src/reporting/ScaffoldLayout.cc ++++ allpathslg-52488/src/reporting/ScaffoldLayout.cc +@@ -21,6 +21,8 @@ + #include <omp.h> + // MakeDepend: library OMP + ++using std::ostringstream; ++ + int main(int argc, char **argv) + { + RunTime( ); +--- allpathslg-52488/src/SeqInterval.cc ++++ allpathslg-52488/src/SeqInterval.cc +@@ -9,6 +9,7 @@ + #include "SeqInterval.h" + #include "Vec.h" + ++using std::min; + + /* + * seq_interval +--- allpathslg-52488/src/SeqInterval.h ++++ allpathslg-52488/src/SeqInterval.h +@@ -14,7 +14,10 @@ + #include <algorithm> + #include <iostream> + +-using namespace std; ++using std::binary_function; ++using std::ostream; ++using std::istream; ++using std::max; + + /* + * class seq_interval +--- allpathslg-52488/src/Set.h ++++ allpathslg-52488/src/Set.h +@@ -16,6 +16,8 @@ + #include <iostream> + #include <set> + ++using std::set; ++ + template <class T, class C=std::less<T>> + using StdSet = std::set<T,C,typename DefaultAllocator<T>::type>; + +--- allpathslg-52488/src/ShortVector.h ++++ allpathslg-52488/src/ShortVector.h +@@ -14,6 +14,8 @@ + #include "system/Types.h" + #include "feudal/BinaryStream.h" + ++using std::uninitialized_fill_n; ++ + // ================================================================================ + // + // A shortvector holds a list of up to 255 things of any type T. +--- allpathslg-52488/src/STLExtensions.h ++++ allpathslg-52488/src/STLExtensions.h +@@ -9,8 +9,6 @@ + #ifndef STLEXTENSIONS_H + #define STLEXTENSIONS_H + +-using namespace std; +- + #include <functional> + #include <vector> + #include <bitset> +@@ -21,6 +19,14 @@ + #include "feudal/BinaryStream.h" + #include "system/StaticAssert.h" + ++using std::binary_function; ++using std::unary_function; ++using std::pair; ++using std::bitset; ++using std::initializer_list; ++using std::vector; ++using std::ostream; ++ + /// minimum<T> is a function object. + /// + /// If f is an object of class minimum<T> and x and y are objects of +--- allpathslg-52488/src/system/MiscUtil.cc ++++ allpathslg-52488/src/system/MiscUtil.cc +@@ -21,6 +21,8 @@ + #include "system/HTMLUtils.h" + #include "system/Utils.h" + ++using std::list; ++ + static Bool makeOnlyIfNeeded = True; + + void SetMakeOnlyIfNeeded( Bool newMakeOnlyIfNeeded ) { +--- allpathslg-52488/src/system/MiscUtil.h ++++ allpathslg-52488/src/system/MiscUtil.h +@@ -27,6 +27,9 @@ + #include "CommonSemanticTypes.h" + #include "graph/Digraph.h" + ++using std::map; ++using std::set; ++ + // Semantic type: shellcmd_t + // The name of a shell command. + SemanticType( String, shellcmd_t ); +--- allpathslg-52488/src/system/ParsedArgs.cc ++++ allpathslg-52488/src/system/ParsedArgs.cc +@@ -26,6 +26,9 @@ + #include "system/HostName.h" + #include "system/UseGDB.h" + ++using std::istrstream; ++using std::mem_fun_ref; ++ + #ifndef FatalErr + #define FatalErr(message) { cout << message << endl << endl; exit(-1); } + #endif +--- allpathslg-52488/src/system/ParsedArgs.h ++++ allpathslg-52488/src/system/ParsedArgs.h +@@ -97,6 +97,8 @@ + #include "TokenizeString.h" + #include "ParseSet.h" + ++using std::stringstream; ++ + class parsed_arg_help { + + public: +--- allpathslg-52488/src/system/ProcBuf.cc ++++ allpathslg-52488/src/system/ProcBuf.cc +@@ -15,6 +15,8 @@ + #include <sys/wait.h> + #include <unistd.h> + ++using std::ios_base; ++ + namespace + { + size_t const BUFFER_SIZE = 8192; +--- allpathslg-52488/src/system/RunTime.cc ++++ allpathslg-52488/src/system/RunTime.cc +@@ -41,6 +41,10 @@ + #include <unwind.h> + #endif + ++using std::strstream; ++using std::hex; ++using std::setw; ++ + /// =========================================================================== + /// + /// ReturnAddress(i), where 0 <= i <= 100: get the return address. The +--- allpathslg-52488/src/system/RunTime.h ++++ allpathslg-52488/src/system/RunTime.h +@@ -14,6 +14,8 @@ + #include "system/Exit.h" + #include "system/Types.h" + ++using std::ostream; ++ + typedef void ArachneSignalHandler(int, siginfo_t*, void*); + + void arachne_signal_handler( int signal_number, siginfo_t* info, void* context, +--- allpathslg-52488/src/system/System.cc ++++ allpathslg-52488/src/system/System.cc +@@ -36,6 +36,10 @@ + + #include <dirent.h> + ++using std::istringstream; ++using std::istream_iterator; ++using std::ostringstream; ++ + int SystemInternal( String command, const char *shell, + int* pStatus, int* pErrNo ) + { +@@ -1088,7 +1092,7 @@ + + bool isReadable( String const& filename ) + { ifstream ifs(filename.c_str()); +- return ifs; } ++ return static_cast<bool>(ifs); } + + int Glob( const String& x, vector<String>& xs ) + { glob_t globbuf; +--- allpathslg-52488/src/system/System.h ++++ allpathslg-52488/src/system/System.h +@@ -21,6 +21,18 @@ + #include "system/Exit.h" + #include "system/file/TempFile.h" + ++using std::vector; ++using std::ostream; ++using std::ofstream; ++using std::ifstream; ++using std::istream; ++using std::ios; ++using std::cout; ++using std::flush; ++using std::endl; ++using std::setprecision; ++using std::fixed; ++ + #ifndef InputErr + #define InputErr(message) \ + cout << "\nFatal error at " << Date() << ": " << message \ +--- allpathslg-52488/src/system/TraceVal.h ++++ allpathslg-52488/src/system/TraceVal.h +@@ -25,6 +25,9 @@ + #include "system/Assert.h" + #include "system/Exit.h" + ++using std::cout; ++using std::endl; ++ + // Macros: Tracing macros + // TRACEVAL_ON - undefine if you're not doing tracing + // TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles +--- allpathslg-52488/src/system/Types.h ++++ allpathslg-52488/src/system/Types.h +@@ -14,7 +14,7 @@ + #include <cstdlib> + #include <netinet/in.h> + +-using namespace std; ++ + + // This assumes that all suns run Solaris... + #if __sun == 1 +--- allpathslg-52488/src/system/WorklistUtils.cc ++++ allpathslg-52488/src/system/WorklistUtils.cc +@@ -32,6 +32,10 @@ + #include <sys/resource.h> + #include <unistd.h> + ++using std::istringstream; ++using std::istream_iterator; ++using std::min; ++ + namespace + { + pthread_t gMainThread; +--- allpathslg-52488/src/util/FastaParser.cc ++++ allpathslg-52488/src/util/FastaParser.cc +@@ -22,6 +22,7 @@ + + using std::string; + using std::vector; ++using std::istringstream; + + char* FastaParser::readLine() + { +--- allpathslg-52488/src/util/FastaParser.h ++++ allpathslg-52488/src/util/FastaParser.h +@@ -24,6 +24,8 @@ + #include <fstream> + #include <vector> + ++using std::max; ++ + /// Base class for the parsers for sequence, quality, and bits which follow. + class FastaParser + { +--- allpathslg-52488/src/util/FastbStats.cc ++++ allpathslg-52488/src/util/FastbStats.cc +@@ -18,6 +18,8 @@ + + #include "random/Random.h" + ++using std::map; ++ + typedef VirtualMasterVec<BaseVec> VBaseVecVec; + + +--- allpathslg-52488/src/util/Happening.cc ++++ allpathslg-52488/src/util/Happening.cc +@@ -25,6 +25,8 @@ + #include "FastIfstream.h" + #include "MainTools.h" + ++using std::istringstream; ++ + vec<String> tracebacks; + Bool TALLYG; + +--- allpathslg-52488/src/util/MemMonitor.cc ++++ allpathslg-52488/src/util/MemMonitor.cc +@@ -21,7 +21,7 @@ + #include <signal.h> + #include <time.h> + +-using namespace std; ++using std::string; + + // convertion factors between jiffies and seconds (check your system!!!) + const double sec_jif = 100.0; +--- allpathslg-52488/src/util/Quala2Qualb.cc ++++ allpathslg-52488/src/util/Quala2Qualb.cc +@@ -11,6 +11,8 @@ + #include "FastIfstream.h" + #include "Qualvector.h" + ++using std::istrstream; ++ + int main(int argc, char *argv[]) + { + RunTime(); +--- allpathslg-52488/src/util/QualbStats.cc ++++ allpathslg-52488/src/util/QualbStats.cc +@@ -20,6 +20,7 @@ + #include "Qualvector.h" + #include "Basevector.h" + ++using std::scientific; + + #define NQ 256 + +--- allpathslg-52488/src/util/ReadTrack.cc ++++ allpathslg-52488/src/util/ReadTrack.cc +@@ -33,6 +33,9 @@ + #include "util/ReadTracker.h" + #include "util/RunCommand.h" + ++using std::map; ++using std::set; ++ + // Return filename portion of path (after last slash) + String basename(const String path) + { +--- allpathslg-52488/src/util/ReadTracker.cc ++++ allpathslg-52488/src/util/ReadTracker.cc +@@ -11,6 +11,9 @@ + #include "VecUtilities.h" + #include "util/ReadTracker.h" + ++using std::string; ++using std::istringstream; ++ + unsigned int + ReadTracker::AddSource(String s) + { +--- allpathslg-52488/src/util/RunCommand.cc ++++ allpathslg-52488/src/util/RunCommand.cc +@@ -14,6 +14,8 @@ + #include <unistd.h> + #include <sstream> + ++using std::ostringstream; ++ + /** + * RunCommand + */ +--- allpathslg-52488/src/util/TextTable.cc ++++ allpathslg-52488/src/util/TextTable.cc +@@ -13,6 +13,8 @@ + #include <sstream> + #include <iterator> + ++using std::max; ++ + vec<vec<String> > TextTable::GetTable( ) const { + vec<vec<String> > table; + for ( size_t i = 0; i < lines.size(); ++i ) { +--- allpathslg-52488/src/util/TextTable.h ++++ allpathslg-52488/src/util/TextTable.h +@@ -33,6 +33,8 @@ + #include "Vec.h" + #include "feudal/TrackingAllocator.h" + ++using std::string; ++ + class TextTable { + public: + // == Special types to draw line and manipulate tables == +--- allpathslg-52488/src/Vec.h ++++ allpathslg-52488/src/Vec.h +@@ -50,6 +50,11 @@ + #include "Compare.h" + #include "system/file/FileReader.h" + ++using std::numeric_limits; ++using std::ostream_iterator; ++using std::setfill; ++using std::setw; ++ + ///////////////////////////////////////////////////////////////////////////// + // + // vec Class Declaration and Template Definitions +--- allpathslg-52488/src/VecOverlap.cc ++++ allpathslg-52488/src/VecOverlap.cc +@@ -12,6 +12,9 @@ + #include "STLExtensions.h" + #include <numeric> + ++using std::max; ++using std::make_pair; ++ + // Represents the suffix of the index'th word starting at the pos'th + // character. + template <class T> +--- allpathslg-52488/src/VecUtilities.h ++++ allpathslg-52488/src/VecUtilities.h +@@ -37,6 +37,9 @@ + #include "Vec.h" + #include <cstddef> + ++using std::less; ++using std::equal_to; ++using std::greater; + + ///////////////////////////////////////////////////////////////////////////// + // diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/allpathslg/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest new file mode 100644 index 000000000000..a849ef2db919 --- /dev/null +++ b/sci-biology/amap/Manifest @@ -0,0 +1,7 @@ +AUX amap-2.2-includes.patch 1088 SHA256 3b22dd095d3dcf674528eb4641f325f7f3e30dc2f8d1173eefa8e1474d1fc5e2 SHA512 e9c2ae7ea75f059b816a8562c9ac79e343d73b9a3d63ac1182fe41b3634bf0b949738a4bdd90c09f61bb4505a721e2faa98334b81ad17c0d7360a2e3f37f9044 WHIRLPOOL fe51978a3a6538e9c57731bfa3b511b342ee95dc93b0fce75f0afef25f6b5d398cf323206e75dac10d0f1bdba538f6a1dfa056d6e0dfa5d68e961579ea6ee863 +AUX amap-2.2-makefile.patch 1201 SHA256 e5ab2e395a610632080c8736bd7e5e91ca36e87ee2165c8b2780772fb85f0cdc SHA512 8cd43b70299e12f32dd6b46a73e6ef10c7e85b5ec6d152aef69f54954a1083c92570c40bf35ea363084a3626161c3e28d214bb2c5fb76bb396d9be2edaa869a3 WHIRLPOOL dbf74ca0a9f32c9bba5e1ccc7346b4de6ffb5b6ff5d4002ee5ed3358b18f2073d917399eb797cb588f78aa97e2c20f94566ca92332e04986c4b72ba46f02e044 +DIST amap.2.2.tar.gz 102861 SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f WHIRLPOOL 2d4b8ff711888bce570aa823e323525b104aef16c57090dc18c3fdcec39a98012b2597b7015bbe9a3626b15d438e488deffcaef96f426fc73a47f10f117c237e +EBUILD amap-2.2-r3.ebuild 1135 SHA256 76f1e79ba6494cab86c84d6549a1b7a653708d40ad87f33523ed26ccb9fa040c SHA512 d5bbb29ad83fd210b3ba7f84884f4bb517d132fbdaa58b658c679cccd96f1219f9fe3d6f8f58a029a10c782e916f441a9e8de969390c168c0202fb230fdb21a1 WHIRLPOOL a7cc931377e49f60abd1daa81dcfbb026e9faa1afcc989e31f328d14282bd4af172ececf659d1e8bade4b0c9b0647f7ea3f5880130099637c27b68e67b54e940 +MISC ChangeLog 2489 SHA256 326205792fcd67fe106972194e905ba9ae25bb794fba715b7fce5199ca999402 SHA512 e21b9c2380fe0cf29d67e329413ee2183fb4af8c4917220ac2d32899be795c7619614d9f9dc57714ebc34512f766f05986a9a8750de16e52a8b12b72f1805d30 WHIRLPOOL 6df50410fe7d249640317502a9b7a4805b2b5df76d5080bb1df9a49ae5c0c9ed40f860f46a15c421c73036d9e2e519d217cbd93bf13eff7982cb19ac6a731d23 +MISC ChangeLog-2015 1909 SHA256 483d897d4db46baf9efcd1e7208f33d86c8fc33c4adbf438751f082034b380a4 SHA512 6307597849b1d2ca56d5f9a4a8f1d59f6ee6bcad9776f0c322844d244c35aa3fa0e52d80ee039dc2e29785194748a2d5e643efade58d27861b105043df70d2c6 WHIRLPOOL e4118bc4e5f0d46a34816927483e6c1de832197c9cbffb739e58062e446ca2ecd1d0313c12a1e1f0af6a1c111d9a0dc8d58c574e290d281460483bcfab6c125b +MISC metadata.xml 257 SHA256 4fb4f49e90ca33b7ed48e29dad0b163cb069e546927f1935e1ef75df1faf0087 SHA512 5be44a06c71b100dfe66effc1d12a9801f6daf2e252f74b6499528644db9b3dd00d51827a984817b78755e8d544f9c674c27c6a370c4c4414ce26a09b478b69b WHIRLPOOL 1ba3dd46c533b22c9b1ac469d0f110149fe5b2081961928d96913b72698c527c317cb17f9ce74451100d7769646b7fd0e3d7c534149474f1d04520704e4e7b1e diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r3.ebuild new file mode 100644 index 000000000000..7776e25bc56e --- /dev/null +++ b/sci-biology/amap/amap-2.2-r3.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit java-pkg-opt-2 java-ant-2 toolchain-funcs + +MY_P=${PN}.${PV} + +DESCRIPTION="Protein multiple-alignment-based sequence annealing" +HOMEPAGE="http://bio.math.berkeley.edu/amap/" +SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="java" + +RDEPEND="java? ( >=virtual/jre-1.5 )" +DEPEND="java? ( >=virtual/jdk-1.5 )" + +S=${WORKDIR}/${PN}-align + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-includes.patch +) + +src_prepare() { + default + java-pkg-opt-2_src_prepare +} + +src_compile() { + emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}" + + if use java; then + pushd display >/dev/null || die + eant -Ddisplay all || die + popd >/dev/null || die + fi +} + +src_install() { + dobin align/${PN} + + dodoc align/{README,PROBCONS.README} + + insinto /usr/share/${PN}/examples + doins -r examples/. + + if use java; then + java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar + java-pkg_dolauncher amapdisplay --jar amapdisplay.jar + fi +} diff --git a/sci-biology/amap/files/amap-2.2-includes.patch b/sci-biology/amap/files/amap-2.2-includes.patch new file mode 100644 index 000000000000..77c4261db5cf --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-includes.patch @@ -0,0 +1,44 @@ +Fixes build with gcc 4.3 and 4.6 + +http://bugs.gentoo.org/217921 +http://bugs.gentoo.org/360517 + +--- amap-align/align/Amap.cc ++++ amap-align/align/Amap.cc +@@ -12,6 +12,8 @@ + #include "ProbabilisticModel.h" + #include "EvolutionaryTree.h" + #include "SparseMatrix.h" ++#include <limits> ++#include <climits> + #include <string> + #include <sstream> + #include <iomanip> +@@ -23,6 +25,7 @@ + #include <cstdlib> + #include <cerrno> + #include <iomanip> ++#include <cstring> + + string parametersInputFilename = ""; + string parametersOutputFilename = "no training"; +--- amap-align/align/MultiSequenceDag.h ++++ amap-align/align/MultiSequenceDag.h +@@ -13,6 +13,7 @@ + #include <map> + #include <queue> + #include <iostream> ++#include <limits> + #include "MultiSequence.h" + #include "SparseMatrix.h" + +--- amap-align/align/SafeVector.h.org 2011-03-26 11:50:11.935069583 +0100 ++++ amap-align/align/SafeVector.h 2011-03-26 11:50:21.112553151 +0100 +@@ -9,6 +9,7 @@ + #define SAFEVECTOR_H + + #include <cassert> ++#include <cstddef> + #include <vector> + + ///////////////////////////////////////////////////////////////// diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch new file mode 100644 index 000000000000..5a9841c98255 --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -0,0 +1,35 @@ +Respect {CXX,LD}FLAGS + +http://bugs.gentoo.org/332009 + +--- amap-align/align/Makefile ++++ amap-align/align/Makefile +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' + + # debug mode +@@ -26,8 +28,7 @@ + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +- ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + ################################################################################ + # 3) Dependencies + ################################################################################ + +@@ -38,7 +37,7 @@ + all : $(TARGETS) + + amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc +- $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm + + .PHONY : clean + clean: diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml new file mode 100644 index 000000000000..e051c9b41035 --- /dev/null +++ b/sci-biology/amap/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> +</maintainer> +</pkgmetadata> diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest new file mode 100644 index 000000000000..5f8f3526e54d --- /dev/null +++ b/sci-biology/amos/Manifest @@ -0,0 +1,10 @@ +AUX amos-3.1.0-fix-build-system.patch 3132 SHA256 1a78682189bcca5b7f896f8c88b63c45cded64dc90210f18ac6be73c39b19ba2 SHA512 b23c168c166f8a1dad89d1b25536a59be3e68a6478cef3db5664dc901cef0547213a8622a72ee1a2e1d5b8930c65d95e309573f903423e8fb80fb7312d89f863 WHIRLPOOL ab6aeb185c2eda629b168df776a9ddfcac611c2458627019459fa2fbdb5dcc393d8751a6e34e319bfe9db092c3df5892b355e18d598ac5f9e133968312d92922 +AUX amos-3.1.0-gcc-4.7.patch 400 SHA256 59be7e1fa3c4125f463e666f304f2194fc73026c71005ac16891e950e75b8af6 SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835 WHIRLPOOL 5c446c940eed42a5d8b47c102e97a4fc3c9818aa40f6049ab6b4e78ee8cf445665afbc78b9c2742e3de3adccb087e8f61ba3ebe567140d2e26d2a6167fe13b65 +AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 SHA256 6dba8f9c13ebabb5aa55c8b6ec71a015315662d00ee749df96e6715b9de45736 SHA512 5d2a0d4b222a23f30db560937b1c0e447f61dc786e097b259696fa41dca1e57a17a1e684bbd9fa9ddcee1334f7e6e3a91ccb7567d4fe079c3bdb3bb54034d11f WHIRLPOOL 3abec572fa4384f7b4d60aa6cb5d3da945e9e78ab462757945e55f7a64440023a229a08ab40b861d9823d7694e5f92683459381865757f9ef284c228ac3409a2 +AUX amos-3.1.0-qa-Wformat.patch 4511 SHA256 afa52695df2d2493089386714acad8d420bcaf64ee0b47273440dac93c43731e SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe WHIRLPOOL 6e9de1a7a01b1cdb4c763205df9544d9653cb309675fa6ad250b033a99c70de24d0f0c1490222e3c18cd07f86cfa4b1946dbf64aab837e54efb61201dc53a5f8 +DIST amos-3.1.0-fix-c++14.patch.bz2 8033 SHA256 23b853959147466e7d766b1fe54e0afabfe3a89b84c89f788f2b8e749344efd6 SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 WHIRLPOOL d4530a5b3ff2a90419a1368a0e652bad367d2fb7601765ca42e8110ade87e8360f90070c0021aa25f5a6421815794a83491581e16fa9cb26be23bcb187840ff3 +DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 +EBUILD amos-3.1.0-r3.ebuild 1089 SHA256 f5fd59da7b6523c22ea79bb235cb88a66899ac20cd58543e6442ab1dc9bfa8fd SHA512 5eaebe166daa11142d77e0d1623a46a0736a1d1180c6bc80ad246f67c684ad38ceba0cf179ea2a7af83c8c2785f24ed12f54c2a71d6a10fe7174f852e649ded8 WHIRLPOOL 25735963c50ebfa80aae91aa21e7effd9ddc67cea56aae9ba0558ff13f555318fdead0e93a796538016acc62fe748fa242fa476ed2d724fc618debce3e571de1 +MISC ChangeLog 2862 SHA256 f41c2ee7fe2ab280c70a7ab4dcfc7996fbaf88168da479b87cd4bb9286a0b68d SHA512 aba67e201ae372c89a3575f1173c9a0145826cba6f421ed6810cd97335ccc375e52e2b146bac6861ea9d061832bd6a7ee1904d4b2bdb3a920cb3ad83e04b20f0 WHIRLPOOL 152c685210d814b0133f14b00627dca6cb88f935429980e1775cda333436182cd09dc5579329b32108b63a68a787f595200457a406ca81617d763aed8f01a69c +MISC ChangeLog-2015 2903 SHA256 acc84b2bce3b80f1badfbd7f077aa6ce126153381202ee7216fc690d71e6ded8 SHA512 4aed01fa4327bf98f4953d3c4007c4b2d2cf97d269f94733233134c21785ba356f915fe907019f862869e79edee801e3d4f4daac0f59feb18cab5e05c87870a0 WHIRLPOOL c7a8ac94dd18417292579f2a4b482877ce64050b2a263a8f0f30db94f36f800949216871e4726773335679c36df3581b189390b4d1280550490001f39343fe0e +MISC metadata.xml 345 SHA256 d071906d7402159bb5834de6e489c5677a5e459e37aa05d0049f83d9e2784c81 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497 WHIRLPOOL 1610108ad99b2b6340c4c7cbf42f5230e0b08513a9efa7bda8030105025e19499c959e1c17ff8ae8aa2bce4f0234ad2b038bfd9840212080ce2edec5a6411a8e diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r3.ebuild new file mode 100644 index 000000000000..ab383a3b95a0 --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r3.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools flag-o-matic python-single-r1 + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="qt4" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + ${PYTHON_DEPS} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch + "${WORKDIR}"/${P}-fix-c++14.patch + "${FILESDIR}"/${P}-qa-Wformat.patch + "${FILESDIR}"/${P}-fix-build-system.patch +) + +src_prepare() { + default + eautoreconf + + # prevent GCC 6 log pollution due + # to hash_map deprecation in C++11 + append-cxxflags -Wno-cpp +} + +src_install() { + default + python_fix_shebang "${ED%/}"/usr/bin/goBambus2 +} diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch new file mode 100644 index 000000000000..9c824dd2f122 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch @@ -0,0 +1,116 @@ +* Use proper AR and not just 'ar' +* Fix build system to build in parallel + +--- a/configure.ac ++++ b/configure.ac +@@ -34,6 +34,7 @@ + AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_RANLIB ++AM_PROG_AR + AC_PROG_CPP + AC_PATH_PROG(PERL, [perl], [:]) + AC_PATH_PROG(PYTHON, [python], [:]) +--- a/src/Align/Makefile.am ++++ b/src/Align/Makefile.am +@@ -133,7 +133,7 @@ + + ##-- hash-overlap + hash_overlap_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +@@ -172,7 +172,7 @@ + + ##-- make-consensus + make_consensus_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +@@ -182,7 +182,7 @@ + + ##-- make-consensus_poly + make_consensus_poly_LDADD = \ +- $(top_builddir)/src/Align/libAlign_poly.a \ ++ libAlign_poly.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +@@ -192,7 +192,7 @@ + + ##-- maligntest + maligntest_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +@@ -202,7 +202,7 @@ + + ##-- merge-contigs + merge_contigs_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +@@ -235,7 +235,7 @@ + + ##-- show-ma-asm + show_ma_asm_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/Common/libCommon.a \ + $(top_builddir)/src/AMOS/libAMOS.a + show_ma_asm_SOURCES = \ +@@ -261,7 +261,7 @@ + + ##-- simple-overlap + simple_overlap_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +@@ -272,7 +272,7 @@ + + ##-- test-align + test_align_LDADD = \ +- $(top_builddir)/src/Align/libAlign.a \ ++ libAlign.a \ + $(top_builddir)/src/CelMsg/libCelMsg.a \ + $(top_builddir)/src/Slice/libSlice.a \ + $(top_builddir)/src/Common/libCommon.a \ +--- a/src/Bambus/Bundler/Makefile.am ++++ b/src/Bambus/Bundler/Makefile.am +@@ -47,7 +47,7 @@ + clk.cc + + MarkRepeats_LDADD = \ +- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ ++ libBundler.a \ + $(top_builddir)/src/Common/libCommon.a \ + $(top_builddir)/src/AMOS/libAMOS.a \ + $(top_builddir)/src/GNU/libGNU.a +@@ -55,7 +55,7 @@ + MarkRepeats.cc + + OrientContigs_LDADD = \ +- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ ++ libBundler.a \ + $(top_builddir)/src/Common/libCommon.a \ + $(top_builddir)/src/AMOS/libAMOS.a \ + $(top_builddir)/src/GNU/libGNU.a +@@ -63,7 +63,7 @@ + OrientContigs.cc + + FilterEdgesByCluster_LDADD = \ +- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ ++ libBundler.a \ + $(top_builddir)/src/Common/libCommon.a \ + $(top_builddir)/src/AMOS/libAMOS.a \ + $(top_builddir)/src/GNU/libGNU.a diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch new file mode 100644 index 000000000000..de2a41184c52 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/Align/find-tandem.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc +index ddf1cab..a29e21e 100644 +--- a/src/Align/find-tandem.cc ++++ b/src/Align/find-tandem.cc +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch new file mode 100644 index 000000000000..97a8f59d0208 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch @@ -0,0 +1,25 @@ +--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 ++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 +@@ -1,7 +1,7 @@ + #pipeline script for assembly + Bambus 2 + #contributed by Todd J Treangen + +-import string, sys, os, subprocess#, spincursor ++import sys, os, subprocess#, spincursor + + RED = "\033[0;31m" + GREEN = "\033[0;32m" +@@ -360,7 +360,7 @@ + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) + +- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) + + if xopt_dict["verbose"] == 1: + print "10) running OutputResults" +@@ -388,4 +388,3 @@ + else: + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) +-) diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch new file mode 100644 index 000000000000..13f4eeb247a1 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch @@ -0,0 +1,136 @@ +Fix QA warnings, due to using incorrect format specifiers in printf: +* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’, +* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=] +* fprintf (stderr, "%u b contigs\n", b . size ()); + +--- a/src/Align/align.cc ++++ b/src/Align/align.cc +@@ -1936,7 +1936,7 @@ + n = align . size (); + con = consensus . c_str (); + +- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); ++ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); + + for (i = 0; i < n; i ++) + { +@@ -3936,7 +3936,7 @@ + } + + // Array of sum of quality scores in the slice for A,C,G,T,- resp. +- for (j = 0; j < 6; j ++) ++ for (j = 0; j < 5; j ++) + qvsum [j] = 0; + + int nof_ambiguities = 0; +--- a/src/Align/align_poly.cc ++++ b/src/Align/align_poly.cc +@@ -1761,7 +1761,7 @@ + n = align . size (); + con = consensus . c_str (); + +- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); ++ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); + for (i = 0; i < n; i ++) + { + fprintf (fp, "\nString #%d:\n", i); +--- a/src/Align/count-qmers.cc ++++ b/src/Align/count-qmers.cc +@@ -191,8 +191,8 @@ + + PrintMers(mer_table, min_count); + +- fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT); +- fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n", LEN); ++ fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT); ++ fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n", LEN); + } + catch (Exception_t & e) + { +--- a/src/Align/kmer-cov.cc ++++ b/src/Align/kmer-cov.cc +@@ -485,7 +485,7 @@ + Kmer_Len = s . length (); + else if (Kmer_Len != int (s . length ())) + { +- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", ++ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", + s . c_str (), s . length (), Kmer_Len); + Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); + } +--- a/src/Align/kmer-cov-plot.cc ++++ b/src/Align/kmer-cov-plot.cc +@@ -316,7 +316,7 @@ + } + else if (Kmer_Len != int (s . length ())) + { +- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", ++ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", + s . c_str (), s . length (), Kmer_Len); + Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); + } +--- a/src/Align/make-consensus.cc ++++ b/src/Align/make-consensus.cc +@@ -303,7 +303,7 @@ + break; + } + +- sprintf (sid, "%ld", ++layout_id); ++ sprintf (sid, "%u", ++layout_id); + cid = string (sid); + ID_t lid = layout.getIID (); + if (lid == 0) +--- a/src/Align/make-consensus_poly.cc ++++ b/src/Align/make-consensus_poly.cc +@@ -279,7 +279,7 @@ + break; + } + +- sprintf(sid, "%ld", ++layout_id); ++ sprintf(sid, "%u", ++layout_id); + cid = string(sid); + ID_t lid = layout.getIID(); + if (lid == 0) { +--- a/src/Align/simple-overlap.cc ++++ b/src/Align/simple-overlap.cc +@@ -422,7 +422,7 @@ + "Options:\n" + " -a Also show alignments of overlaps \n" + " -E <x> Maximum error rate for overlaps is <x>\n" +- " e.g., -E 0.06 for 6% error rate\n" ++ " e.g., -E 0.06 for 6%% error rate\n" + " -F Input is a fasta file\n" + " -h Print this usage message\n" + " -o <n> Set minimum overlap length to <n>\n" +--- a/src/Compare/contig-cmp.cc ++++ b/src/Compare/contig-cmp.cc +@@ -145,7 +145,7 @@ + + fclose (fp); + +- fprintf (stderr, "%u a contigs\n", a . size ()); ++ fprintf (stderr, "%zu a contigs\n", a . size ()); + vector <Unitig_t> a_contig (max_id + 1); + n = a . size (); + for (i = 0; i < n; i ++) +@@ -234,7 +234,7 @@ + + fclose (fp); + +- fprintf (stderr, "%u b contigs\n", b . size ()); ++ fprintf (stderr, "%zu b contigs\n", b . size ()); + vector <Unitig_t> b_contig (max_id + 1); + n = b . size (); + for (i = 0; i < n; i ++) +--- a/src/Staden/progs/trace_convert.c ++++ b/src/Staden/progs/trace_convert.c +@@ -6,6 +6,9 @@ + #include "traceType.h" + #include "seqIOABI.h" + ++#include <fcntl.h> ++#include <unistd.h> ++ + static char fileIdentifier[] = "$Id$"; + + struct opts { diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml new file mode 100644 index 000000000000..2668bce2ac8a --- /dev/null +++ b/sci-biology/amos/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">amos</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/arb/Manifest 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000000000000..f52beded359c --- /dev/null +++ b/sci-biology/arb/arb-5.1-r1.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=2 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + mirror://gentoo/${P}-glibc2.10.patch.bz2 + https://dev.gentoo.org/~jlec/${P}-linker.patch.bz2" + +LICENSE="arb" +SLOT="0" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +RDEPEND="${DEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-glibc2.10.patch\ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/${PV}-libs.patch \ + "${FILESDIR}"/${PV}-bfr-overflow.patch + sed -i \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -e 's/--export-dynamic/-Wl,--export-dynamic/g' \ + "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links || die +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" || die +} diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild new file mode 100644 index 000000000000..a7388bf9b816 --- /dev/null +++ b/sci-biology/arb/arb-5.2.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2" + +SLOT="0" +LICENSE="arb" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +CDEPEND="app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +DEPEND="${CDEPEND} + sys-process/time" +RDEPEND="${CDEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/5.1-libs.patch \ + "${FILESDIR}"/5.1-bfr-overflow.patch \ + "${FILESDIR}"/${PV}-libpng15.patch \ + "${FILESDIR}"/${P}-gcc-47.patch + sed \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -e 's:-O4::g' \ + -e 's:-pipe::g' \ + -i "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" +} diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild new file mode 100644 index 000000000000..135bec2695ce --- /dev/null +++ b/sci-biology/arb/arb-5.3.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz" + +SLOT="0" +LICENSE="arb" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +CDEPEND="app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +DEPEND="${CDEPEND} + sys-process/time" +RDEPEND="${CDEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/5.1-libs.patch \ + "${FILESDIR}"/5.1-bfr-overflow.patch \ + "${FILESDIR}"/5.2-libpng15.patch \ + "${FILESDIR}"/${PN}-5.2-gcc-47.patch + sed \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -i "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" +} diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch new file mode 100644 index 000000000000..21d21f5ac17f --- /dev/null +++ b/sci-biology/arb/files/5.1-bfr-overflow.patch @@ -0,0 +1,16 @@ + ARB_GDE/GDE_HGLfile.cxx | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx +index e353a89..f69635a 100644 +--- a/ARB_GDE/GDE_HGLfile.cxx ++++ b/ARB_GDE/GDE_HGLfile.cxx +@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type) + if(this_elem->id[0] == '\0') + strncpy(this_elem->id,uniqueID(),79); + if(this_elem->short_name[0] == '\0') +- strncpy(this_elem->short_name,this_elem->id,79); ++ strncpy(this_elem->short_name,this_elem->id,31); + if(this_elem->seqlen == 0) + this_elem->protect= + PROT_BASE_CHANGES+ diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch new file mode 100644 index 000000000000..bf0bacad3286 --- /dev/null +++ b/sci-biology/arb/files/5.1-libs.patch @@ -0,0 +1,16 @@ +diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl +index b653a66..b346c96 100644 +--- a/SOURCE_TOOLS/provide_libs.pl ++++ b/SOURCE_TOOLS/provide_libs.pl +@@ -118,11 +118,6 @@ sub provide_libs($$$) { + foreach my $lib (keys %needed_by) { + update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir); + } +- if ($opengl==1) { +- foreach my $lib (keys %needed_by_opengl) { +- update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir); +- } +- } + } + + sub main() { diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch new file mode 100644 index 000000000000..3d750e76efe3 --- /dev/null +++ b/sci-biology/arb/files/5.2-libpng15.patch @@ -0,0 +1,45 @@ +Fix building with libpng-1.5 + +https://bugs.gentoo.org/show_bug.cgi?id=378353 + +Patch written by Samuli Suominen <ssuominen@gentoo.org> +--- a/GL/glpng/glpng.c ++++ b/GL/glpng/glpng.c +@@ -285,7 +285,7 @@ + endinfo = png_create_info_struct(png); + + // DH: added following lines +- if (setjmp(png->jmpbuf)) ++ if (setjmp(png_jmpbuf(png))) + { + png_destroy_read_struct(&png, &info, &endinfo); + return 0; +@@ -390,7 +390,7 @@ + endinfo = png_create_info_struct(png); + + // DH: added following lines +- if (setjmp(png->jmpbuf)) ++ if (setjmp(png_jmpbuf(png))) + { + png_destroy_read_struct(&png, &info, &endinfo); + return 0; +@@ -569,7 +569,7 @@ + #define ALPHA *q + + switch (trans) { +- case PNG_CALLBACK: ++ case PNG_CALLBACKT: + FORSTART + ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b); + FOREND +--- a/GL/glpng/glpng.h ++++ b/GL/glpng/glpng.h +@@ -57,7 +57,7 @@ + #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS + + /* Transparency parameters */ +-#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */ ++#define PNG_CALLBACKT -3 /* Call the callback function to generate alpha */ + #define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */ + #define PNG_SOLID -1 /* No transparency */ + #define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */ diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch new file mode 100644 index 000000000000..186e78e450b3 --- /dev/null +++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch @@ -0,0 +1,15 @@ + AWTI/AWTI_import.cxx | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx +index 8e730ac..e3f9ff4 100644 +--- a/AWTI/AWTI_import.cxx ++++ b/AWTI/AWTI_import.cxx +@@ -12,6 +12,7 @@ + #include <GEN.hxx> + + #include <climits> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/arb/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest new file mode 100644 index 000000000000..f65f5231299d --- /dev/null +++ b/sci-biology/ariadne/Manifest @@ -0,0 +1,7 @@ +AUX ariadne-1.3-gcc4.patch 207 SHA256 8362c7cc50340129e7c2f76ebf6333b15c59d4a6e01f24b40ba0032370987b0e SHA512 81750d979dbabe25867daba2dd658eeb1a8e1c04560d2fc067ece20dc3e92abaf98aceefd769c79be87bfcfb18902cb2042a3abbf9c47f79ff281a02b0a9d249 WHIRLPOOL f862b3c59938fedc947c5bd2706aac30dfba582f3831bed05bd25d4f0064d2bc961b7073e3c025e7303ae55b612ea7ea548402af02f329edf538b1d802de3363 +AUX ariadne-1.3-implicits.patch 480 SHA256 994186ec3843ab228e00f3c30c96e5830dfe76da91a7ef59d58f75e6ec2536da SHA512 014dddcf7c3c107ecd77acb9d0110c50bf864cfa20959283ae868a74116d333e2a09749291882f12fffaabed34773e52c9cba5d0b7e476d1e8a14a7df5091a84 WHIRLPOOL 1690e687a4e04ceb59207c55a6a0011d28147843fa29120cec9bcf6ab24e31f1daca9406e2b6162dfb4463173b75eb754626366b7a424a7e6a44aaa791023dfb +DIST ariadne-1.3.tar.Z 69427 SHA256 8b6b0acb6e8d02b1303d94b20906bf2bf1dee3de4eceeb1b927cfba7a96fd00d SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289 WHIRLPOOL 460d8acf2bb49e097a9544ecc089ca60c3478b64ab4d903bd6ee801eccd62fc560bdccf1454c9f22632081cbf1df35de09a4f81d6c131d3f52f36753bc692927 +EBUILD ariadne-1.3-r3.ebuild 904 SHA256 2b02c45f7d4e66da3684cef162ee77bfa190e68daac3ec63a4ca75544a683811 SHA512 eceba1b9bf54353df40f061deaa6925034d4bf029a735adce713e20a93a014fc921bfe50cd1caf1befce59348d7f15cbb5d4fe52f220534b05d8c1b3592adaf6 WHIRLPOOL 7425e55a035c7ddf741738387f0e71499adf1bfbf6cf7e950b44ddefda4fe36c7d90a66a962602cfbd38acba8077a3965b13a58e5e1564fce3978516a6743103 +MISC ChangeLog 2555 SHA256 40a8883ae9a28fb0016421f602f8552bfbeb2ea870748397eca80ea7318be879 SHA512 bccf46011df1058beabac685cfebb37063f87e88cdcae1cc7b0bcc8a140ae1053c702fb4f72a4276656f89d1ec2ca139b459c23bf750caedd4dcd1bcbba304cd WHIRLPOOL 5024abd3b8608abedef84f70af53479829c24d8e91128a0f10e87d959ed1bc0c1de5972624aa7dc21ba319dff939a7618db1a3ce188286aebef8f084c322fa22 +MISC ChangeLog-2015 2027 SHA256 65cc77f47568411aa45c916571e6dafafa339568ebcb235cc99cf0f7be9d9a6d SHA512 a63f1a231c2096a8bced1076b9a733e06824ed481de950929d3749cd90a77b61254b47efecb426196ec66daf5b25bce068b45d1c38ac04d26e446cc3427d8f5a WHIRLPOOL b00873b5b4bb252e3d8b860cacd030e7db9460b2a2b86880479c9debde6b5fe23b3c5d051685bf53be7b1e7e15caed0fa69ce94682007d26961777c3bb9914f6 +MISC metadata.xml 954 SHA256 aef3dabcfb12e924a2557c41f1e043866b164b90bab8f731347d239c4fb7df0e SHA512 07101ae5c65d25810f0b32e5bef44b2ee078e858e17ee4b1351f444dc95ad746417f3684206c94487c6203bfcdafc5b0c67b17a1fb5fbfd4ba7a74009bfd2743 WHIRLPOOL b41dfc704c477aced682fabc75d70d93376b33e31ca0432fcbcafa2886641b69291cc55ff149f71edbf33f69725d3e0261cdb97269977a9b9412d3910e08f825 diff --git a/sci-biology/ariadne/ariadne-1.3-r3.ebuild b/sci-biology/ariadne/ariadne-1.3-r3.ebuild new file mode 100644 index 000000000000..0103c6d3648c --- /dev/null +++ b/sci-biology/ariadne/ariadne-1.3-r3.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Protein sequences and profiles comparison" +HOMEPAGE="http://www.well.ox.ac.uk/ariadne/" +SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z" + +LICENSE="ARIADNE" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/SRC-${PV} + +PATCHES=( + "${FILESDIR}"/${P}-gcc4.patch + "${FILESDIR}"/${P}-implicits.patch +) + +src_prepare() { + default + sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045 + sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die +} + +src_compile() { + emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}" +} + +src_install() { + dobin Linux/{ariadne,prospero} + + use static-libs && dolib.a Linux/libseq.a + + insinto /usr/include/${PN} + doins Include/*.h + + einstalldocs +} diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch new file mode 100644 index 000000000000..8bda75cb4f3a --- /dev/null +++ b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch @@ -0,0 +1,10 @@ +--- a/cl.c ++++ b/cl.c +@@ -658,6 +658,7 @@ + fclose(fp); + if ( ! stat( filename, &buf ) ) + { ++ char *ctime(), *t; + sprintf( date, "%s", ctime(&buf.st_mtime) ); + t = date; + while ( *t ) diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch new file mode 100644 index 000000000000..31c442b12265 --- /dev/null +++ b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch @@ -0,0 +1,23 @@ +topalign.c:96:5: warning: implicit declaration of function ‘toupper’ +prospero.c:63:3: warning: implicit declaration of function ‘strcpy’ + +--- SRC-1.3/prospero.c ++++ SRC-1.3/prospero.c +@@ -26,6 +26,7 @@ + */ + + #include<stdio.h> ++#include<string.h> + #include<math.h> + #include"cl.h" + #include"seq_util.h" +--- SRC-1.3/topalign.c ++++ SRC-1.3/topalign.c +@@ -26,6 +26,7 @@ + */ + + #include<stdio.h> ++#include<ctype.h> + #include<math.h> + #include"seq_util.h" + #include"ariadne.h" diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml new file mode 100644 index 000000000000..d0e8e0be55e0 --- /dev/null +++ b/sci-biology/ariadne/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + ARIADNE is a package of two programs, ariadne and prospero, that + compare protein sequences and profiles using the Smith-Waterman + algorithm, and assesses statistical significance using a new accurate + formula, described in Mott, 2000, "Accurate Formula for P-values of + gapped local sequence and profile alignments" J. Mol Biol. 300:649-659. + The sequence/profile comparison algorithms used in ARIADNE are + standard, and are probably not the fastest implementations available. + The novel part is the method for determining statistical significance, + which will give thresholds of significance that are accurate to within + 5% 95% of the time. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000000..ff0fe1247ee3 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1,6 @@ +AUX augustus-2.5.5-sane-build.patch 5271 SHA256 0e8692203f1cc994398bc639d101b2be915c4747a5d234d0d564cf0ada6e9ebc SHA512 5afe12b51b8ce27ef32e8e66dd72be451022757228b4c86dec938b26870885bee06712438a22801a42944d2def8ae8bf4a2d7fdb82e12455c145abcd6f0c4aa1 WHIRLPOOL f6bde27abe50c567a2a07ef61ce9c8033592261b26a61828eac9f6d6e74b104220a986d9bd57138b74375a747e2b9c619a49e7a6865be4de037a288b7882186b +DIST augustus.2.5.5.tar.gz 70826249 SHA256 2bd97784fa651addf836e2100a7d4106b43e50fe06f13c664001d4625d0eab9a SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f WHIRLPOOL 875f56f10251767fb066b5e21b0c2361c952d5cc44daa811658be8119957ffa34fd4552fde7e17384d5bc916aee5ef91982ded3999d0077cf3834d5fc20e7f1a +EBUILD augustus-2.5.5.ebuild 1010 SHA256 033f5e2e2b896c957d5d8967453e0b1b96f678f29868c8b5eb851eecbd8df0c1 SHA512 6cf6076dd9c1c957302f5ec65867b9055a29e4a893f925bc18cb96cc7c57509e65497013e574a33dbe718f0aeb4a25422078874cf0b85603b30ca40abe81527f WHIRLPOOL 2bb05518431d7bdd3668ec1d6a2b176c2ef1dfcb7d64795ff8cc3cbc17de24b92673f85070f0fd456010a5be31660366863240d105cf2280c2cceafea2df3e7a +MISC ChangeLog 2473 SHA256 2c4273e98146a8dc38d829552338065b456a56e357159e132118fdf965ede5d8 SHA512 062913083dad8dac702b249e13c9ca47dd724251bc87ee8544b2e22e5a8dab6e85359a285da508d039187907df52ed34ba6f9c99550d9517f7b07425278dc5ef WHIRLPOOL dc3e0173575eeb291afb2e72623c1e13919f3c9b6ecf2bf25fd59d2e98114b55b146cd36e1b7d5facbdd8c72125911d0812309e7b83ff06cdbcb250e0f88db49 +MISC ChangeLog-2015 2694 SHA256 e16526a6f364e77aee894fdebdf37d30122ab4160720c02958d7f5da49a5d431 SHA512 6c32e0eca978ac36d1eeaca4bb8319ea279789709a09ebe00dcd3af6e581c877d1f09a6391e3c92fc0d616354bb7c6661c961a13d2256f7df5a14f8c3874d5c7 WHIRLPOOL e01995e98d2882ce11571bb9c9990de20d80d1fe22a126f295fde66b36fbedd2f5c3e3dfa00d898c2c59a3c5799018c6729a459cbb697f9ddbda24f6a5a3c4f6 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild new file mode 100644 index 000000000000..ff4dfd6cc7e0 --- /dev/null +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="examples" + +S="${WORKDIR}/${PN}.${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-sane-build.patch + tc-export CC CXX +} + +src_compile() { + emake clean && emake +} + +src_install() { + dobin bin/* +# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} + + exeinto /usr/libexec/${PN} + doexe scripts/*.p* + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi +} diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch new file mode 100644 index 000000000000..39cd0762b1c1 --- /dev/null +++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch @@ -0,0 +1,156 @@ + Makefile | 8 +++--- + scripts/Makefile | 6 +++- + scripts/aln2wig/Makefile | 8 +++--- + scripts/compileSpliceCands/Makefile | 6 ++-- + src/Makefile | 43 ++++++++++++++++++---------------- + 5 files changed, 38 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index e23a667..64610c8 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,9 +3,9 @@ + # + + all: +- cd src && ${MAKE} +- cd scripts && ${MAKE} ++ $(MAKE) -C src ++ $(MAKE) -C scripts + + clean: +- cd src && ${MAKE} clean +- cd scripts && ${MAKE} clean ++ $(MAKE) -C src clean ++ $(MAKE) -C scripts clean +diff --git a/scripts/Makefile b/scripts/Makefile +index 6d4dd67..ab6a885 100644 +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,5 +1,7 @@ + all : +- cd aln2wig && ${MAKE} ++ $(MAKE) -C aln2wig ++ $(MAKE) -C compileSpliceCands + + clean : +- cd aln2wig && ${MAKE} clean ++ $(MAKE) -C aln2wig clean ++ $(MAKE) -C compileSpliceCands +diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile +index 64d09f5..9752980 100644 +--- a/scripts/aln2wig/Makefile ++++ b/scripts/aln2wig/Makefile +@@ -1,10 +1,10 @@ +-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb ++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic + + psl2wig : aln2wig.o +- gcc $(CFLAGS) -o aln2wig aln2wig.o; +- cp aln2wig ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o; ++ cp aln2wig ../../bin/ + psl2wig.o : aln2wig.c +- gcc $(CFLAGS) -c aln2wig.c ++ $(CC) $(CFLAGS) -c aln2wig.c + + all : psl2wig + +diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile +index cddada5..8079791 100644 +--- a/scripts/compileSpliceCands/Makefile ++++ b/scripts/compileSpliceCands/Makefile +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc -o compileSpliceCands compileSpliceCands.o list.o; +-# cp compileSpliceCands ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ cp compileSpliceCands ../../bin/ + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi -c compileSpliceCands.c ++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c + + all : compileSpliceCands + +diff --git a/src/Makefile b/src/Makefile +index 71795b6..732b953 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,8 +6,8 @@ + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. + # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh) + # +-CC = g++ +-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static ++CXX ?= g++ ++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static + INCLS = -I../include -I. + LIBS = # -lcwd + OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ +@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte + PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign + INFO = cflags + +-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info ++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin + + .SUFFIXES: + .SUFFIXES: .cc .o .so + + .cc.o: +- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS) ++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) + +-augustus: augustus.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++bin: $(PROGR) ++ cp $(PROGR) ../bin/ ++ ++augustus: augustus.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp augustus ../bin/ + +-etraining: etraining.cc $(TOBJS) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++etraining: etraining.o $(TOBJS) $(OBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp etraining ../bin/ + +-evaluate: evaluate.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++evaluate: evaluate.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-consensusFinder: consensusFinder.cc consensus.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++consensusFinder: consensusFinder.o consensus.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-curve2hints: curve2hints.cc exon_seg.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++curve2hints: curve2hints.o exon_seg.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \ ++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \ + types.o properties.o geneticcode.o pp_profile.o lldouble.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp fastBlockSearch ../bin/ + +-prepareAlign: pp_prepare_align.cc +- $(CC) $(CFLAGS) -o $@ $^ ++prepareAlign: pp_prepare_align.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ + cp prepareAlign ../bin/ + + info: +- echo "$(CFLAGS)" > $(INFO) ++ echo "$(CXXFLAGS)" > $(INFO) + + clean: +- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/* + + tidy: clean + rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO) diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/augustus/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest new file mode 100644 index 000000000000..2437568ff360 --- /dev/null +++ b/sci-biology/bamtools/Manifest @@ -0,0 +1,7 @@ +AUX bamtools-2.4.1-fix-build-system.patch 7559 SHA256 6f4de0efe1f415e530424244ec74c5f058dbcabd1345a1a8f81d0e11673b8b5b SHA512 41b16e6eaba5c6008ad0ff620ba7adf036ef03c9cf881e269e837274957a770608a25f20d1f01dfec91e318a994682299465273b6904f7c16f6b9544e909db78 WHIRLPOOL 81762b619ecb1bb75e8a6894d38ec465181fd261e254935ed199aa30dbfba8c321f22bb22bea0ea4f1270a49b374aa58f1dc4fd5c078ecd394958a73c7a55515 +AUX bamtools-2.4.1-fix-c++14.patch 2584 SHA256 f9a0e39c7f0c146eb2366deff7c4c7143f18d8b0ead5cfbe0f58f45f8a14c592 SHA512 e583ee9241df351e814c4de9297c7513e7cae3155e71a16f35aac1191c57dd2abc0c1eb166131660b8583a9a96bb0a7ccda2aa6048d5f098e07671f7232a5c7b WHIRLPOOL f92dc2b63598c7a0fa1a43994a68bc5ca4d2d5c5844d25ae3001be8f9a6b0d882717211f7f972c509c933226d2a6e07597f37380073f7388eedc81a8f5c8800f +DIST bamtools-2.4.1.tar.gz 540482 SHA256 933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b SHA512 ee674014f27b2dc0aa7c0415e8654ee7c39cfdecafbd9983d970fad6ad29f070a7ff372ee05765956cf7c8f8bb3b9763b6e537e693a0d2d64680148b1a23cfee WHIRLPOOL 6ef73f0713ebf993123eac7095061e32fe6a53db383e28a5dd8967afee92fb211ce56611de9718ce4cce84bdee14157ff968e0a6edcaead4e06b44008b78b84c +EBUILD bamtools-2.4.1.ebuild 588 SHA256 109334524441860441a7e2dad37664b53497866f29ad9a7cce7f8f95c3577072 SHA512 d9140d0315a7b37662f2c9ffc40f42ef450925e55458f3af31f6048b48610ad721622f970eb3f9d9df5d011c339c1eee4ce0e9b13ccb16a6954156497c92258e WHIRLPOOL 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4922e3edaa65c7981b8656245287e4c4d613f8ba6d6b63131fe9e5183f8119eab5501e354ad80d37d8f61f56d86513af2aedd2b086e5da3d1ab48b3aef57a18c WHIRLPOOL 979a222333a4c0073a7105e9593aa139541735a27fda813101d0c187a470112ff94a78042f5a11b3601bf680c5cd75ace3f06117fbd045dc7627d2c30e5f38e2 diff --git a/sci-biology/bamtools/bamtools-2.4.1.ebuild b/sci-biology/bamtools/bamtools-2.4.1.ebuild new file mode 100644 index 000000000000..2196c66790d3 --- /dev/null +++ b/sci-biology/bamtools/bamtools-2.4.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" +HOMEPAGE="https://github.com/pezmaster31/bamtools" +SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + >=dev-libs/jsoncpp-1.8.0 + sys-libs/zlib" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.4.1-fix-build-system.patch + "${FILESDIR}"/${PN}-2.4.1-fix-c++14.patch +) diff --git a/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch b/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch new file mode 100644 index 000000000000..795972330303 --- /dev/null +++ b/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch @@ -0,0 +1,209 @@ +* Unbundle jsoncpp +* Remove forcing C++98 +* Remove forcing CMAKE_BUILD_TYPE +* Remove -fPIC globally +* Fix LFS macro definitions +* Make building static library optional +* Use GNUInstallDirs conventions +* Install .pc file +See also: https://bugs.gentoo.org/show_bug.cgi?id=550144 + +Taken from https://github.com/pezmaster31/bamtools/pull/139 + +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -9,7 +9,14 @@ + project( BamTools ) + + # Cmake requirements +-cmake_minimum_required( VERSION 2.6.4 ) ++cmake_minimum_required( VERSION 3.0 ) ++ ++# on macOS, MACOSX_RPATH is enabled by default on more recent versions ++# of CMake. Disable this behaviour, and let user enable it if need be. ++cmake_policy( SET CMP0042 OLD ) ++ ++# Adhere to GNU filesystem layout conventions ++include( GNUInstallDirs ) + + # Force the build directory to be different from source directory + macro( ENSURE_OUT_OF_SOURCE_BUILD MSG ) +@@ -34,18 +41,21 @@ + set( BamTools_VERSION_MINOR 4 ) + set( BamTools_VERSION_BUILD 1 ) + +-# set our library and executable destination dirs +-set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" ) +-set( LIBRARY_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/lib" ) +- + # define compiler flags for all code +-set( CMAKE_BUILD_TYPE Release ) +-set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" ) +-add_definitions( -Wall -D_FILE_OFFSET_BITS=64 ) ++add_definitions( -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE ) ++add_compile_options( -Wall ) + + # ----------------------------------------------- + # handle platform-/environment-specific defines + ++# Make building the static library optional ++option( BUILD_STATIC "Build static libbamtools archive" OFF ) ++if( BUILD_STATIC ) ++ set( BAMTOOLS_CMD_LDFLAGS BamTools-static ) ++else() ++ set( BAMTOOLS_CMD_LDFLAGS BamTools ) ++endif() ++ + # If planning to run in Node.js environment, run: + # cmake -DEnableNodeJS=true + if( EnableNodeJS ) +@@ -57,6 +67,11 @@ + add_definitions( -DSUN_OS ) + endif() + ++# find system JsonCpp ++find_package( PkgConfig ) ++pkg_search_module( JSONCPP jsoncpp>=1 ) ++ ++ + # ------------------------------------------- + + # add our includes root path +--- a/src/api/CMakeLists.txt ++++ b/src/api/CMakeLists.txt +@@ -10,7 +10,6 @@ + + # add compiler definitions + add_definitions( -DBAMTOOLS_API_LIBRARY ) # (for proper exporting of library symbols) +-add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake) + + # fetch all internal source files + add_subdirectory( internal ) +@@ -31,18 +30,6 @@ + ${InternalSources} + ) + +-# create main BamTools API shared library +-add_library( BamTools SHARED ${BamToolsAPISources} ) +-set_target_properties( BamTools PROPERTIES +- SOVERSION "2.4.1" +- OUTPUT_NAME "bamtools" ) +- +-# create main BamTools API static library +-add_library( BamTools-static STATIC ${BamToolsAPISources} ) +-set_target_properties( BamTools-static PROPERTIES +- OUTPUT_NAME "bamtools" +- PREFIX "lib" ) +- + # link libraries automatically with zlib (and Winsock2, if applicable) + if( WIN32 ) + set( APILibs z ws2_32 ) +@@ -50,12 +37,23 @@ + set( APILibs z ) + endif() + +-target_link_libraries( BamTools ${APILibs} ) +-target_link_libraries( BamTools-static ${APILibs} ) ++# create main BamTools API shared library ++add_library( BamTools SHARED ${BamToolsAPISources} ) ++set_target_properties( BamTools PROPERTIES ++ SOVERSION "2.4.1" ++ OUTPUT_NAME "bamtools" ) ++target_link_libraries( BamTools ${APILibs} ) ++install( TARGETS BamTools LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ) + +-# set library install destinations +-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") +-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") ++# create main BamTools API static library ++if( BUILD_STATIC ) ++ add_library( BamTools-static STATIC ${BamToolsAPISources} ) ++ set_target_properties( BamTools-static PROPERTIES ++ OUTPUT_NAME "bamtools" ++ PREFIX "lib" ) ++ target_link_libraries( BamTools-static ${APILibs} ) ++ install( TARGETS BamTools-static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" ) ++endif() + + # export API headers + include(../ExportHeader.cmake) +--- a/src/bamtools.pc.in ++++ b/src/bamtools.pc.in +@@ -0,0 +1,11 @@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@ ++ ++Name: BamTools ++Description: BamTools is a C++ library for reading and manipulating BAM files ++Version: @BamTools_VERSION_MAJOR@.@BamTools_VERSION_MINOR@.@BamTools_VERSION_BUILD@ ++ ++Libs: -L${libdir} -lbamtools ++Cflags: -I${includedir} +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -14,3 +14,7 @@ + include( ExportHeader.cmake ) + set( SharedIncludeDir "shared" ) + ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} ) ++ ++# configure and install pkg-config file ++configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools.pc.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc @ONLY ) ++install( FILES ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig ) +--- a/src/ExportHeader.cmake ++++ b/src/ExportHeader.cmake +@@ -18,10 +18,10 @@ + add_custom_command( TARGET ${MODULE} COMMAND + ${CMAKE_COMMAND} -E copy_if_different + "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}" +- "${CMAKE_SOURCE_DIR}/include/${DEST}/${FILENAME}" ) ++ "${CMAKE_CURRENT_BINARY_DIR}/include/${DEST}/${FILENAME}" ) + + # make sure files are properly 'installed' +- install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" ) ++ install( FILES "${FILE}" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/bamtools/${DEST}" ) + + endfunction( ExportHeader ) + +--- a/src/third_party/CMakeLists.txt ++++ b/src/third_party/CMakeLists.txt +@@ -5,5 +5,3 @@ + # src/third-party/ + # ========================== + +-# list third-party subdirectories to build in +-add_subdirectory( jsoncpp ) +--- a/src/toolkit/CMakeLists.txt ++++ b/src/toolkit/CMakeLists.txt +@@ -35,10 +35,14 @@ + OUTPUT_NAME "bamtools" + ) + # make version info available in application +-configure_file( bamtools_version.h.in ${BamTools_SOURCE_DIR}/src/toolkit/bamtools_version.h ) ++configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools_version.h.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools_version.h ) ++include_directories( ${CMAKE_CURRENT_BINARY_DIR} ) ++ ++# set include paths for system JsonCpp ++target_include_directories( bamtools_cmd PRIVATE ${JSONCPP_INCLUDE_DIRS} ) + + # define libraries to link +-target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) ++target_link_libraries( bamtools_cmd BamTools-utils ${BAMTOOLS_CMD_LDFLAGS} ${JSONCPP_LDFLAGS} ) + + # set application install destinations +-install( TARGETS bamtools_cmd DESTINATION "bin") ++install( TARGETS bamtools_cmd DESTINATION "${CMAKE_INSTALL_BINDIR}" ) +--- a/src/utils/CMakeLists.txt ++++ b/src/utils/CMakeLists.txt +@@ -8,9 +8,8 @@ + # list include paths + include_directories( ${BamTools_SOURCE_DIR}/src/api ) + +-# add compiler definitions ++# add compiler definitions + add_definitions( -DBAMTOOLS_UTILS_LIBRARY ) # (for proper exporting of library symbols) +-add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake) + + # create BamTools utils library + add_library( BamTools-utils STATIC diff --git a/sci-biology/bamtools/files/bamtools-2.4.1-fix-c++14.patch b/sci-biology/bamtools/files/bamtools-2.4.1-fix-c++14.patch new file mode 100644 index 000000000000..8d9b1e02c19f --- /dev/null +++ b/sci-biology/bamtools/files/bamtools-2.4.1-fix-c++14.patch @@ -0,0 +1,78 @@ +* Fix building in C++11/C++14 modes +See also: https://bugs.gentoo.org/show_bug.cgi?id=596208 + +Taken from https://github.com/pezmaster31/bamtools/pull/139 + +--- a/src/api/BamConstants.h ++++ b/src/api/BamConstants.h +@@ -126,10 +126,10 @@ + + // zlib & BGZF constants + const char GZIP_ID1 = 31; +-const char GZIP_ID2 = 139; ++const char GZIP_ID2 = static_cast<char>(139); + const char CM_DEFLATE = 8; + const char FLG_FEXTRA = 4; +-const char OS_UNKNOWN = 255; ++const char OS_UNKNOWN = static_cast<char>(255); + const char BGZF_XLEN = 6; + const char BGZF_ID1 = 66; + const char BGZF_ID2 = 67; +--- a/src/toolkit/bamtools_filter.cpp ++++ b/src/toolkit/bamtools_filter.cpp +@@ -16,7 +16,7 @@ + #include <utils/bamtools_utilities.h> + using namespace BamTools; + +-#include <jsoncpp/json.h> ++#include <json/json.h> + using namespace Json; + + #include <cstdio> +@@ -647,7 +647,7 @@ + if ( !reader.parse(document, root) ) { + // use built-in error reporting mechanism to alert user what was wrong with the script + cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl +- << reader.getFormatedErrorMessages(); ++ << reader.getFormattedErrorMessages(); + return false; + } + +--- a/src/toolkit/bamtools_resolve.cpp ++++ b/src/toolkit/bamtools_resolve.cpp +@@ -410,7 +410,7 @@ + ReadGroupResolver& resolver = (*rgIter).second; + + // store read name with resolver +- resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ; ++ resolver.ReadNames.insert( make_pair(fields[1], true) ) ; + } + + // if here, return success +@@ -607,7 +607,7 @@ + resolver.IsAmbiguous = ( fields.at(6) == TRUE_KEYWORD ); + + // store RG entry and return success +- readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) ); ++ readGroups.insert( make_pair(name, resolver) ); + return true; + } + +@@ -1014,7 +1014,7 @@ + } + + // if read name not found, store new entry +- else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) ); ++ else resolver.ReadNames.insert( make_pair(al.Name, isCurrentMateUnique) ); + } + + // close files +@@ -1046,7 +1046,7 @@ + SamReadGroupConstIterator rgEnd = header.ReadGroups.ConstEnd(); + for ( ; rgIter != rgEnd; ++rgIter ) { + const SamReadGroup& rg = (*rgIter); +- m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) ); ++ m_readGroups.insert( make_pair(rg.ID, ReadGroupResolver()) ); + } + } + diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml new file mode 100644 index 000000000000..f703e6a82899 --- /dev/null +++ b/sci-biology/bamtools/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>proxy-maint@gentoo.org</email> + <name>Proxy Maintainers</name> + </maintainer> + <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> + <upstream> + <remote-id type="github">pezmaster31/bamtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest new file mode 100644 index 000000000000..9f3fa1a6c35f --- /dev/null +++ b/sci-biology/bcftools/Manifest @@ -0,0 +1,5 @@ +AUX bcftools-1.5-buildsystem.patch 376 SHA256 fe15af0cd646dbb51041f78d00287696ec70d19b592f8f1f9967b373a81ffbca SHA512 c8ede2be5205ab287843662e7b97ecae8d4fc7d2aaf09e0b9fa67f5a3168149b15457e73c2c9d8b74fcfada08ec5c1bbe61013a2ef434ee50acf56eccabf6723 WHIRLPOOL 590ff61577c5b55c553d37dbe7a421fa71c4f4c5648df8aff45d68027ee419574400d7660aee29f5f586fe73f3fad2bfe7893c3954c242a02d8d0c2faf00bc8f +AUX bcftools-1.5-fix-shebangs.patch 594 SHA256 a2360809840fe2683c0c85edae8977f62eaa923b77c66921c69031ab35e8b7a7 SHA512 e00cc0de35ad5866f7321408a7995f054f80e37e642b6c3097c5e786635dc61baefa7ea8847f2222d32196825e3e44209d63fdfd219c54b09421a4bb310067f5 WHIRLPOOL 1589c582746650f357a3c28428e3900a2b6e56c3ea7bc538f4dc141cfb5112b467020e3da52886e4ad54929a02e72bd3411185ff623860062cf9a17309e42e1c +DIST bcftools-1.5.tar.bz2 2975685 SHA256 9ff75a680891467776d7064f41deb6be7a595030ba807494727cd5bee7842301 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233 WHIRLPOOL 86b827d91351d8adc026a1d851bb708e35febcc36a947532662857787ec1da6eea2c88a684b15164638b7f9235f6a6f92f4d10618e1719aa891c44c69aaece77 +EBUILD bcftools-1.5.ebuild 868 SHA256 0fe3b3b2d2fa16dd56ecb5bc23f10726795ceb1b94feebd05bf596f60610bfef SHA512 e0aacba5fc54cbf7a8d64db84e52f28baf8df36fa01c63fc167998c6ec5ef65a040c0725f445970f32888ae947b89d50d92dc2fc704fdf63a8a900762ec367e6 WHIRLPOOL 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+HOMEPAGE="http://www.htslib.org" +SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-${PV}*:= + sys-libs/zlib + ${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.5-buildsystem.patch + "${FILESDIR}"/${PN}-1.5-fix-shebangs.patch +) + +src_prepare() { + default + + # remove bundled htslib + rm -r htslib-* || die +} + +src_configure() { + econf \ + --disable-bcftools-plugins \ + --disable-libgsl \ + --disable-configure-htslib \ + --with-htslib=system +} diff --git a/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch new file mode 100644 index 000000000000..304fc03e7441 --- /dev/null +++ b/sci-biology/bcftools/files/bcftools-1.5-buildsystem.patch @@ -0,0 +1,10 @@ +--- a/Makefile ++++ b/Makefile +@@ -275,7 +275,6 @@ + $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) + $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) +- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir) + + clean: testclean clean-plugins + -rm -f gmon.out *.o *~ $(PROG) version.h plugins/*.so plugins/*.P diff --git a/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch new file mode 100644 index 000000000000..c6cfc8b991d3 --- /dev/null +++ b/sci-biology/bcftools/files/bcftools-1.5-fix-shebangs.patch @@ -0,0 +1,24 @@ +--- a/misc/guess-ploidy.py ++++ b/misc/guess-ploidy.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2.7 + # + # Plot the output of "bcftools +guess-ploidy -v" + # +--- a/misc/plot-roh.py ++++ b/misc/plot-roh.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python2.7 + + import glob, gzip, csv, sys, os, copy, re + csv.register_dialect('tab', delimiter='\t', quoting=csv.QUOTE_NONE) +--- a/misc/vcfutils.pl ++++ b/misc/vcfutils.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright (C) 2010 Broad Institute. + # Copyright (C) 2011, 2014 Genome Research Ltd. diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml new file mode 100644 index 000000000000..4fd13be2f922 --- /dev/null +++ b/sci-biology/bcftools/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">samtools/bcftools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest new file mode 100644 index 000000000000..42dfe1981f0b --- /dev/null +++ b/sci-biology/beast-mcmc/Manifest @@ -0,0 +1,6 @@ +DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5 +EBUILD beast-mcmc-1.7.5-r1.ebuild 2906 SHA256 9f36131b95bf15763235e913fe720760f217e6c789b352cdf0cee32d82ca870f SHA512 1bc83f37bd0bfd2477bcf31e7206d1d4337c24123870a407aac2b2ac69ea65d52958930dd2d5c9c961b862f3e7935356809aefbadc8938b7798125b4ebec7ac0 WHIRLPOOL ba33e77030a822941599a9311e079ddd669407201f8065f467ca3eef06c1b5f4da435dd45505eef9037c2946efb6313ff94569bd3e2e7f5f79cca9bfa44ceedd +EBUILD beast-mcmc-9999.ebuild 2743 SHA256 72a683da9d25129601f93d486b7539c9d9d01afaac322742147199ef169b1629 SHA512 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+EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +#inherit java-pkg-2 java-ant-2 eutils subversion +inherit java-pkg-2 java-ant-2 eutils + +MY_P=BEASTv${PV} + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="https://github.com/beast-dev/beast-mcmc" +#SRC_URI="" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS=" + dev-java/colt:0 + dev-java/jdom:0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/release/Linux/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die + #rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom + java-pkg_jar-from colt + java-pkg_jar-from itext +# java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-2 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) +} diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild new file mode 100644 index 000000000000..824d891c6f2f --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="2" + +ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +inherit java-pkg-2 java-ant-2 eutils subversion + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="https://github.com/beast-dev/beast-mcmc" +SRC_URI="" +#SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS="dev-java/colt:0 + dev-java/jdom:0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom + java-pkg_jar-from colt + java-pkg_jar-from itext + java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-1 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples || die + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml new file mode 100644 index 000000000000..18e746ab76ff --- /dev/null +++ b/sci-biology/beast-mcmc/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">beast-dev/beast-mcmc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest new file mode 100644 index 000000000000..7c948a833063 --- /dev/null +++ b/sci-biology/bedtools/Manifest @@ -0,0 +1,6 @@ +AUX bedtools-2.26.0-fix-buildsystem.patch 26994 SHA256 a008b90271114e999f23607a98bf0a069dc64aa5ae2511ede2c6fd6569ab6e10 SHA512 16b4994a9e3bad0a17f0be94fe9412c6c8aee2b5d909007c655fcf3de60c221d3f9ddbe558df7e54466481910d5fa9b871b8123d9bdb1e7c695682990d2457f4 WHIRLPOOL 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58422d02e2baffe394db4dc914dc1985917c429c5a39a7c29f4238bb707ce30dbd45ef542de20451623a21e9e24ad8a0ba482577d9f0c2f8da1fa99b2fbfc95c WHIRLPOOL add4afc88654155e9c8a5be5760fc51923e58c1e72e26236015c2d0515041f473c12dc266adc11feae5cbe92db286c2da2f1aa2bd0e6d61fb579c1addf534bb2 +MISC ChangeLog-2015 1271 SHA256 d1b4c752bd7af15afd10e1daeaa15b4e2a65d196043b13f292f6e95004b3f55e SHA512 dc761058ac65528750f49160eb143d88fd3b4bb24df639e83c0293614e4d88a7a08bf274c549ad7a242459588d15675a760616f491c1ac31ce90de13edc7d512 WHIRLPOOL 7792d1d4af1450e663db0ed687158c67107a5fa9b912740e57173765702fd96412d4fcad8109564c433ca15566ee9e97ca205aae2855aececb45f46719bf3699 +MISC metadata.xml 761 SHA256 31b82efb7f094f9830ec864ca143ad2c4898ab46462c47287a3e223b640d595c SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770 WHIRLPOOL e588f733faf174b57a9cf0a4af112fd68031171726942f80eff5ea69b58239fff06b8dee9c8ce7eb79eb18dfd5ea3ef51159295aa68ae36af8162f3268676688 diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild new file mode 100644 index 000000000000..eeedf606debe --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) + +inherit flag-o-matic python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="test" + +DEPEND="${PYTHON_DEPS} + test? ( + sci-libs/htslib + sci-biology/samtools:0 + )" +RDEPEND="sys-libs/zlib" + +S="${WORKDIR}/${PN}2" + +DOCS=( README.md RELEASE_HISTORY ) +PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) + +src_configure() { + append-lfs-flags + export prefix="${EPREFIX}/usr" + tc-export AR CXX +} + +src_install() { + default + + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch new file mode 100644 index 000000000000..fb6be18d7071 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch @@ -0,0 +1,869 @@ +* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308) +* Remove CXX and CXXFLAGS, ebuild sets them +* Handle python via Gentoo's EPYTHON instead + +--- a/Makefile ++++ b/Makefile +@@ -16,17 +16,9 @@ + export BIN_DIR = bin + export SRC_DIR = src + export UTIL_DIR = src/utils +-export CXX = g++ +-ifeq ($(DEBUG),1) +-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG +-else +-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) +-endif + export LIBS = -lz + export BT_ROOT = src/utils/BamTools/ + +-prefix ?= /usr/local +- + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ + $(SRC_DIR)/bamToFastq \ +@@ -135,13 +127,13 @@ + + all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) + @echo "- Building main bedtools binary." +- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) +- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) + @echo "done." + + @echo "- Creating executables for old CLI." +- @python scripts/makeBashScripts.py +- @chmod +x bin/* ++ $(EPYTHON) scripts/makeBashScripts.py ++ chmod +x bin/* + @echo "done." + + +--- a/src/annotateBed/Makefile ++++ b/src/annotateBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/bamToBed/Makefile ++++ b/src/bamToBed/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bamToFastq/Makefile ++++ b/src/bamToFastq/Makefile +@@ -24,7 +24,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/bed12ToBed6/Makefile ++++ b/src/bed12ToBed6/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bedpeToBam/Makefile ++++ b/src/bedpeToBam/Makefile +@@ -33,7 +33,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ +--- a/src/bedToBam/Makefile ++++ b/src/bedToBam/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bedToIgv/Makefile ++++ b/src/bedToIgv/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/closestFile/Makefile ++++ b/src/closestFile/Makefile +@@ -40,7 +40,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/clusterBed/Makefile ++++ b/src/clusterBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/complementFile/Makefile ++++ b/src/complementFile/Makefile +@@ -42,7 +42,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/coverageFile/Makefile ++++ b/src/coverageFile/Makefile +@@ -38,7 +38,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/expand/Makefile ++++ b/src/expand/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/fastaFromBed/Makefile ++++ b/src/fastaFromBed/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/fisher/Makefile ++++ b/src/fisher/Makefile +@@ -51,7 +51,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/flankBed/Makefile ++++ b/src/flankBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/genomeCoverageBed/Makefile ++++ b/src/genomeCoverageBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/getOverlap/Makefile ++++ b/src/getOverlap/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/groupBy/Makefile ++++ b/src/groupBy/Makefile +@@ -42,7 +42,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/intersectFile/Makefile ++++ b/src/intersectFile/Makefile +@@ -39,7 +39,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/jaccard/Makefile ++++ b/src/jaccard/Makefile +@@ -43,7 +43,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/linksBed/Makefile ++++ b/src/linksBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/mapFile/Makefile ++++ b/src/mapFile/Makefile +@@ -38,7 +38,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/maskFastaFromBed/Makefile ++++ b/src/maskFastaFromBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/mergeFile/Makefile ++++ b/src/mergeFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/multiBamCov/Makefile ++++ b/src/multiBamCov/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/multiIntersectBed/Makefile ++++ b/src/multiIntersectBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/nekSandbox1/Makefile ++++ b/src/nekSandbox1/Makefile +@@ -35,7 +35,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/nucBed/Makefile ++++ b/src/nucBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/pairToBed/Makefile ++++ b/src/pairToBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/pairToPair/Makefile ++++ b/src/pairToPair/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/randomBed/Makefile ++++ b/src/randomBed/Makefile +@@ -23,7 +23,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/regressTest/Makefile ++++ b/src/regressTest/Makefile +@@ -24,24 +24,18 @@ + # ---------------------------------- + # define our source and object files + # ---------------------------------- +-#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h +-#OBJECTS= regressTestMain.o RegressTest.o +-#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) ++SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h ++OBJECTS= regressTestMain.o RegressTest.o ++BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + PROGRAM= regressTest + +- +-all: #$(BUILT_OBJECTS) +- @echo "compiling RegressTest.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) +- @echo "compiling regressTestMain.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++all: $(BUILT_OBJECTS) + + .PHONY: all + +-#$(BUILT_OBJECTS): $(SOURCES) +-# @echo " * compiling" $(*F).cpp +-# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) +- ++$(BUILT_OBJECTS): $(SOURCES) ++ @echo " * compiling" $(*F).cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/reldist/Makefile ++++ b/src/reldist/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/sampleFile/Makefile ++++ b/src/sampleFile/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/shiftBed/Makefile ++++ b/src/shiftBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/shuffleBed/Makefile ++++ b/src/shuffleBed/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/slopBed/Makefile ++++ b/src/slopBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/sortBed/Makefile ++++ b/src/sortBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/spacingFile/Makefile ++++ b/src/spacingFile/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/split/Makefile ++++ b/src/split/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/subtractFile/Makefile ++++ b/src/subtractFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/tagBam/Makefile ++++ b/src/tagBam/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/unionBedGraphs/Makefile ++++ b/src/unionBedGraphs/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/BamTools/Makefile ++++ b/src/utils/BamTools/Makefile +@@ -56,12 +56,12 @@ + + $(LIBRARY): $(OBJECTS) + @echo " * linking $(LIBRARY)" +- ar cr $@ $^ ++ $(AR) cr $@ $^ + -ranlib $@ + + $(OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp + + .PHONY: api + api: +--- a/src/utils/BamTools-Ancillary/Makefile ++++ b/src/utils/BamTools-Ancillary/Makefile +@@ -21,7 +21,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/bedFile/Makefile ++++ b/src/utils/bedFile/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/bedFilePE/Makefile ++++ b/src/utils/bedFilePE/Makefile +@@ -17,7 +17,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/bedGraphFile/Makefile ++++ b/src/utils/bedGraphFile/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/BinTree/Makefile ++++ b/src/utils/BinTree/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/BlockedIntervals/Makefile ++++ b/src/utils/BlockedIntervals/Makefile +@@ -23,7 +23,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/chromsweep/Makefile ++++ b/src/utils/chromsweep/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/Contexts/Makefile ++++ b/src/utils/Contexts/Makefile +@@ -36,7 +36,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/driver/Makefile ++++ b/src/utils/driver/Makefile +@@ -85,7 +85,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/Fasta/Makefile ++++ b/src/utils/Fasta/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/FileReaders/Makefile ++++ b/src/utils/FileRecordTools/FileReaders/Makefile +@@ -32,7 +32,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/FileReaders/Makefile~ ++++ b/src/utils/FileRecordTools/FileReaders/Makefile~ +@@ -31,7 +31,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/Makefile ++++ b/src/utils/FileRecordTools/Makefile +@@ -34,9 +34,9 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling FileRecordMgr.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp + @echo " * compiling FileRecordMergeMgr.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp + + + +--- a/src/utils/FileRecordTools/Records/Makefile ++++ b/src/utils/FileRecordTools/Records/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/fileType/Makefile ++++ b/src/utils/fileType/Makefile +@@ -22,7 +22,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/general/Makefile ++++ b/src/utils/general/Makefile +@@ -21,7 +21,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/GenomeFile/Makefile ++++ b/src/utils/GenomeFile/Makefile +@@ -20,9 +20,9 @@ + + $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS) + @echo " * compiling GenomeFile.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp + @echo " * compiling NewGenomeFile.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp + + #$(EXT_OBJECTS): + # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ +--- a/src/utils/gzstream/Makefile ++++ b/src/utils/gzstream/Makefile +@@ -38,7 +38,7 @@ + UTILITIES_DIR = ../../utils/ + + ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h +- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C + + clean: + @echo "Cleaning up." +--- a/src/utils/KeyListOps/Makefile ++++ b/src/utils/KeyListOps/Makefile +@@ -31,7 +31,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + $(EXT_OBJECTS): +--- a/src/utils/NewChromsweep/Makefile ++++ b/src/utils/NewChromsweep/Makefile +@@ -34,7 +34,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/RecordOutputMgr/Makefile ++++ b/src/utils/RecordOutputMgr/Makefile +@@ -29,7 +29,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/sequenceUtilities/Makefile ++++ b/src/utils/sequenceUtilities/Makefile +@@ -17,7 +17,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/tabFile/Makefile ++++ b/src/utils/tabFile/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/ToolBase/Makefile ++++ b/src/utils/ToolBase/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/VectorOps/Makefile ++++ b/src/utils/VectorOps/Makefile +@@ -11,7 +11,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/version/Makefile ++++ b/src/utils/version/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) $(HEADERS) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/windowBed/Makefile ++++ b/src/windowBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/windowMaker/Makefile ++++ b/src/windowMaker/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml new file mode 100644 index 000000000000..39869a9f2790 --- /dev/null +++ b/sci-biology/bedtools/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>proxy-maint@gentoo.org</email> + <name>Proxy Maintainers</name> + </maintainer> + <longdescription> + BEDTools: a flexible suite of utilities for comparing genomic features. + </longdescription> + <upstream> + <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest new file mode 100644 index 000000000000..ae8b11de2851 --- /dev/null +++ b/sci-biology/bfast/Manifest @@ -0,0 +1,5 @@ +DIST bfast-0.7.0a.tar.gz 2456617 SHA256 ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836 WHIRLPOOL f9098c00a2f328fd5116447aae86f0aed078f6c2e6a49a4459e09f0c2a2023e0d60be1893fc2337b85444c24efb2636953517eda2ced336d1bc6dc8d94706e6b +EBUILD bfast-0.7.0a.ebuild 878 SHA256 ec3a4a2eb673c05e4cbb0fff60357484ab8299d29a0bf0618a096377c1e70877 SHA512 1250f77e618c3164126e584cb85efec65afb4a8884ea30c8b4418ee812907824945bbc945893e48eb45c21ee3b082efb235616c891507c3494e81341c804693c WHIRLPOOL 446f781c13823263183403d9bb54df384f36523cc77d748287ff473ee03ce442b79354d098c960d63fdbcff904840892633f9c9ee972dbae1f94e68de1feb190 +MISC ChangeLog 2656 SHA256 763af98b24b15cd0cdbdbbd55fc573d40d0857557e5e8be7e318bb7769c24d87 SHA512 b3f402df9dc4e3c17b1a9176febbb511214535e96eac8e7805193728a253e2026d394eb807a25985166f94e618f024533eea7d12dae5d889be032cecfa613e28 WHIRLPOOL 613b72c5454e16ab0e387508856c7790378e34d0707ef709c18665388dc28dec5f36cbf74b60e61ca3e374c11f81d989b40a1b94a78cdbf61328fd174b12b02f +MISC ChangeLog-2015 1764 SHA256 300764a645e32c9b02d739f44ad8a482ef89543de3bbc1bacfe827822d8aceba SHA512 e188df2ab81e95fe0b3425936f96bb73625ead148decfd16ca955df1fe43b94365339a3ae607e23fe7d60ef018e1a78967537311ec3cd17498693107fb5752ba WHIRLPOOL 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+HOMEPAGE="https://sourceforge.net/projects/bfast/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="test" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="dev-perl/XML-Simple" + +src_prepare() { + sed \ + -e 's/-m64//' \ + -e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \ + -e 's:-g -O2::g' \ + -i configure.ac || die + sed \ + -e 's:. test.definitions.sh:. ./test.definitions.sh:g' \ + -i tests/*sh || die + + sed \ + -e '/docdir/d' \ + -i Makefile.am || die + + use test && AUTOTOOLS_IN_SOURCE_BUILD=1 + + append-flags -fgnu89-inline + + autotools-utils_src_prepare +} diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml new file mode 100644 index 000000000000..933dea84e1b3 --- /dev/null +++ b/sci-biology/bfast/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bfast</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/biogrep/Manifest b/sci-biology/biogrep/Manifest new file mode 100644 index 000000000000..768ae234be61 --- /dev/null +++ b/sci-biology/biogrep/Manifest @@ -0,0 +1,6 @@ +DIST biogrep-1.0.pdf 22179 SHA256 87f6a0952a2ebba43fff265d2396851d0be0b578fa94ff11f7dc0427bf784528 SHA512 b0430bded7529a14e3e551e4c7deeffdbdbbe674b5a4bd68afa359b2a4e9f0b8fb4a6474673d298508fa728cf83a328327860e60b3777e92afb15fa87f076411 WHIRLPOOL 02e4c3cc8dfc15f48107731d8515df60e4bde0546eb93cb20bcefb22a1da4a7d7aef05ad7225330e1b276ad7bd34ac7cc1ff2dbbb76a75631c90679cf821c68b +DIST biogrep-1.0.tar.gz 71867 SHA256 15421d79f6f16d6bf9bef132a97f7f9ede1bd42d3fb90572df04a1e1abd8cfd8 SHA512 da07ea6f5f6fd601a94dc1b9495b204affcdc4d5e7fedfebbb65d6382ef0573e43b4ebd081c24909b2790ec2ae532505604112d4943c3e4e6575e13bdcdf1ae3 WHIRLPOOL 3b73e1d0908a7ceebe72a2660c2b13df168449d246411e1a29b3b910951c9932f86f3a829499bc53c22a6b6881097d846bfa6bd95968f246a669076c798af173 +EBUILD biogrep-1.0-r2.ebuild 866 SHA256 fc2988a8d36935d9cf577200fe42ce313b1fe5302f2e437e1b7a2ad7609aed9d SHA512 224009fb74306670ecff19a0c9d271608aadb20fea285ff9146c8e45c08918629c3ab0176388b6dfadbbd07fb462e1b4d8cc5f1dff93957dfdefde0f4e780fb9 WHIRLPOOL 1483439a2eb5f39610b3b67b93547b985fb3640664d4ae8331af0014f4f280140c326e232a28ce173c8d94a0d710929c9f4b422102e7d5a1d7ab223248b1d74b +MISC ChangeLog 3407 SHA256 4625c3cab68494c5b28ee284fa17c4d843e40aba147ca08d8b9ecd725459632c SHA512 bcf44fe91b4bb5c85bb43ff4857b2b3a8c9a0f4b4e18e2c0ed64a74395dfb0aedd52622e2e74ee15df43c1be22340c8ce52ee515c2f6c4ed134e6522144e630d WHIRLPOOL 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000000000000..55c780b9ddef --- /dev/null +++ b/sci-biology/biogrep/biogrep-1.0-r2.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Multithreaded tool for matching large sets of patterns against biosequence DBs" +HOMEPAGE="http://stephanopoulos.openwetware.org/BIOGREP.html" +SRC_URI="http://www.openwetware.org/images/3/3d/${P^}.tar.gz -> ${P}.tar.gz + doc? ( http://www.openwetware.org/images/4/49/${PN^}.pdf -> ${P}.pdf )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples" + +src_prepare() { + default + mv configure.{in,ac} || die + eautoreconf +} + +src_install() { + use doc && DOCS+=( "${DISTDIR}"/${P}.pdf ) + if use examples; then + # remove cruft before installing examples + find examples/ \( -name 'CVS' -o -name '*~' \) -exec rm -rf '{}' + || die + + DOCS+=( examples ) + docompress -x /usr/share/doc/${PF}/examples + fi + + default +} diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-biology/biogrep/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest new file mode 100644 index 000000000000..2cddccb0241f --- /dev/null +++ b/sci-biology/biopandas/Manifest @@ -0,0 +1,6 @@ +DIST biopandas-0.1.4.tar.gz 5386 SHA256 0cc9e43e2ddcb0c33448660ee2ed2db02694e57daa1875d004525c40633a6d95 SHA512 efd7ec94bbcc069d8bf0d160480e7ef2c7c0f9febe21a684b46b6b14c69cebb0b3d9f2c315897be6b0ae888ed40731e2f5a16dee45b9c932b05c2c0209b62b84 WHIRLPOOL 1429e59bbb1b29ba116864e577d4be2f1b988e3a82b07c65525eae825b2a742b52da86ed49c837ba461814abf79f2e70d0ea43ee7d4f7906d6a38b39f0ad98f4 +DIST biopandas-0.2.1.tar.gz 209379 SHA256 8952e1177d09b920b24d71e2a83ee76cbbd08055dd2672a366f03cc4fa9678c8 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8 WHIRLPOOL 9f3d088fde230cbc8c9efc25e06430ab8ea87a7050bcbb26bba1b3bb2ef2a300d7f9ebd77490652423a93b517f604156af6f11bde1702b7187c849b171f030f6 +EBUILD biopandas-0.1.4.ebuild 1067 SHA256 0bd60f84ad2424c1f94a4a51410f5a1856dc832a68734037648ac9e7415ad4c3 SHA512 9bd16c56d2a85d3f7e5db4c5eca0bbe73aec7ba975e0391cf4dba848f25cdc97a5ddab21ee1581fdfb15026fb9d5b9edbda5d65a33013c25f35741b4c9e19acf WHIRLPOOL f743a095f03f7537c2534d5fa080f7ec897615c20f24f25c7b00bddc0e70ca079ea46399d80a55255dbb4be6203fb74cb9b53c7bb6226f63c5a0177942d2d7bb +EBUILD biopandas-0.2.1.ebuild 1069 SHA256 45d58ed934f0ce74e1394a3d36192776d5c9b828caa82c7e791b1276aae1ade7 SHA512 c22c2233f8cc176f67f4a3786067549fdb59f589ece5e23d78254ec570ce220bdc0e7f39a3061a3d8b91c54f974993742450c644c444aa957b805d5ad4332c43 WHIRLPOOL 17c3169ad20636a3c62e051e65d758e9340369c510e6388ed87dace615ae6b7a383e089922ffd3f870f6dc438b98e17202e304b11916112ea0be5fa94c818446 +MISC ChangeLog 1574 SHA256 009f6b8a3e7c56e5559e39d7d026cbb6e9c1da701cb7c5e7f647a4fcb5ff4254 SHA512 4fb19e0d4e7385832f07f36fa2bc339d60917712a39ef389b7c63c9ede5a0ef9ce7f0de85e12a7af433108cba98d999abd643602a4e81c6e9b3ef7fb6003a403 WHIRLPOOL e46a971d8ee4eb73a8d012554bfb25ee17b5a0273e2a1cbf1e418083dd65c462220b59cbdaca544ad19648cd88f96f6b2e45ad16f66d2fb6bd06892011e29c9d +MISC metadata.xml 536 SHA256 9bdf3beeb62721b0d155c944ebbf18f7218f507aec62f7d506971f2e440e7ce0 SHA512 502803e30ecfac53516b56501a7bffeb49c3c0bc44ce5b3dd87aac5c745de614c235523ba3be374fcbede1a9a7bcf11c328abb27d82e087b275303f38b80b166 WHIRLPOOL fc29057d37ae21422dbcd6d9bc03af90940630ba872d5c68f747e1d4f235d9aaccc0acb55e1495cffd640a5ff1e5c576506e727e382ee0b69e7aabe914ea256f diff --git a/sci-biology/biopandas/biopandas-0.1.4.ebuild b/sci-biology/biopandas/biopandas-0.1.4.ebuild new file mode 100644 index 000000000000..26e41891d0b2 --- /dev/null +++ b/sci-biology/biopandas/biopandas-0.1.4.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{4,5} ) + +inherit distutils-r1 + +MY_PN="BioPandas" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Molecular Structures in Pandas DataFrames" +HOMEPAGE=" + https://rasbt.github.io/biopandas/ + https://github.com/rasbt/biopandas + https://pypi.python.org/pypi/BioPandas" +SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( + dev-python/nose[${PYTHON_USEDEP}] + )" + +python_test() { + "${EPYTHON}" --version + "${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" + "${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" + "${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" + nosetests -s --verbose ${PN} || die +} diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.1.ebuild new file mode 100644 index 000000000000..5243039d53b6 --- /dev/null +++ b/sci-biology/biopandas/biopandas-0.2.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 + +MY_PN="BioPandas" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Molecular Structures in Pandas DataFrames" +HOMEPAGE=" + https://rasbt.github.io/biopandas/ + https://github.com/rasbt/biopandas + https://pypi.python.org/pypi/BioPandas" +SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( + dev-python/nose[${PYTHON_USEDEP}] + )" + +python_test() { + "${EPYTHON}" --version + "${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" + "${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" + "${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" + nosetests -s --verbose ${PN} || die +} diff --git a/sci-biology/biopandas/metadata.xml b/sci-biology/biopandas/metadata.xml new file mode 100644 index 000000000000..f23da0b1ebe2 --- /dev/null +++ b/sci-biology/biopandas/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">BioPandas</remote-id> + <maintainer status="unknown"> + <email>mail@sebastianraschka.com</email> + <name>Sebastian Raschka</name> + </maintainer> + <remote-id type="github">rasbt/biopandas</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest new file mode 100644 index 000000000000..6cb8843176a4 --- /dev/null +++ b/sci-biology/bioperl-db/Manifest @@ -0,0 +1,8 @@ +AUX bioperl-db-1.6.9-db.patch 1567 SHA256 8ae757084e0f2b1933da271921ede70bed2a0408c179108b62520b2433a4f493 SHA512 a0a2ca951645b70b2e4eb3390598b2a42d6631109500238d6fc482d97a616ec1881738e5dc9af118d37fdf50657916ff275124f409510cf15515dfbc829766c0 WHIRLPOOL 0e5eaeed9248ca9581e4ed20f8ad616e12947e75e97f6ee4d0ded580d74c1a606a78b8352337c7accd42e3f5709e602c4694f97e44a9ef106fce57343bdd8cea +DIST BioPerl-DB-1.006900.tar.gz 492799 SHA256 50df2447b7f3e26aebcf02ed7344d3ef562c3f5393c1584a8ae086185c8c9139 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 WHIRLPOOL b484ce9f464a7189e5b2fffd6facdd426e8b9009ffca5e1661986490bc45dc0269faec5e9eeebdb23ec5c706f62a670fbb6bfc5a60b11c268c7e6f34bf1f03f2 +EBUILD bioperl-db-1.6.9-r1.ebuild 2024 SHA256 58f6b9583d0f68d1cce6cdf6093719aa384f96be474b3694bc83e5e89d28a9f3 SHA512 91814c0b622e2390ac3db18bed47d4ea5f02f7fe493a668bab9a5de4ec3735c64385d4b11ca21d34a05f476e30b7fce7100b3fab77d51607b78804f9b23451e0 WHIRLPOOL d95ba2f87c25536d5ebdcfe89fa7eeb127c07fd2429b01647e3fa5f54d064120fc27f4bc089e1237035baf70245c07ffa5e2cbf318cf5cc998947ec3c775352e +EBUILD bioperl-db-1.6.9.ebuild 914 SHA256 3a4b5008b5fba0376a25b252fbe860c585922a9c6161bc1038f7262d2746050b SHA512 0d555ef35d5a6e9fda3a48ffc3c7437ad52110c8c9f2a223f103c15c6a866c6c776b7c8d0b1c5c1848336263c64a6e79f80ba476d6205e8f3a90788236ff13e8 WHIRLPOOL 01cb04c656c944eb23b3d3c741e887663b6605872b612c134a6a89129460eb3241d5f731bf4d84fb06acc5f6df6be64dcfba54156854ba1e8208fbdac2ac65c4 +EBUILD bioperl-db-9999-r1.ebuild 811 SHA256 81ad8e871f3da8ce9e8135baaf69d5d07b13fedc8bd5a2b2912a3367580b24fa SHA512 23c57f3cf36d0be73470941b408ef59e84457b9db37cb764ba9553bb38404c48498665982a827c981328b6e37b8e7429170644a51ef3d8e9bbd2fe468f8ca7d8 WHIRLPOOL b40c5193ff19433435dbd7fca3ac0018c6e0d91f05f46b7f8dacb0bfac70ca34407f148a9ade41650562c3e7d0a78793c645adfc9d3f0242dec09ceb610af303 +MISC ChangeLog 2501 SHA256 eb07657ab421bb85f4f77009b0e5918ad4752a507e79bcfb166d7cbe1dc6e49a SHA512 d71c1f72dc281a5c1bfdc9f706cabd8e12816094a2481d79f48d37b0444b42801becefc7a94a7d0867498f618b80b873ad77256e4469cb55353ea46e281eb3e4 WHIRLPOOL b58d0a4f108826b26b2953005629e74fc1da6640877104988a842b04fa0ca3bb6dc36b6d73f3ac42b8c23da5a6e1b4844c06160e77c812029b37ae469497140e +MISC ChangeLog-2015 2319 SHA256 cc5e31c7b46436054b18d1d2b6d020c68080dc59e9c807857e81fbfbdf72a1ef SHA512 dc3f7e0d92bd8984a83aed5a5fe739f24cf2e96f53087af0f6d36c6a441102733f109c22da0e960c8b2815a133b99a2129c448077e36f7a5f9a368386f302aa5 WHIRLPOOL 62459d94d25fcbe5ccfdc3ffb4316600acd1389cb2ebaebc927f2680e8aca56d955ff2cb02183cb754efc048e6fd751108fed81aba97683573f383ce0f1b69d1 +MISC metadata.xml 344 SHA256 1b450924ccc444666839a3700e9ac18a38f8f99db0cbeedd5f4e202466edd564 SHA512 a477289255247669c332915665c4d414ba2857b5716a60e8aec1bf8d1c38009c9fcfb7421a02bdbd9ad566be32bf2b21f57fd21c745aa62185d5dcd13d78bf70 WHIRLPOOL e29a2e18f1d081a4624730b992858c71d1124a7c320b76cdbb2ec422f3071c67c6a0cc0d14aa0c731fec643a5f44270f67441913b8b26f454677bc9aa5a9e2f4 diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild new file mode 100644 index 000000000000..facab7d5ffbe --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +BIOPERL_RELEASE=1.6.9 + +DIST_NAME=BioPerl-DB +DIST_AUTHOR=CJFIELDS +DIST_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +RESTRICT="test" +IUSE="test" + +DIST_TEST="do" # Parallelism probably bad +PATCHES=( "${FILESDIR}/${PN}-1.6.9-db.patch" ) +RDEPEND=" + >=sci-biology/bioperl-${PV} + dev-perl/DBD-mysql + dev-perl/DBI + sci-biology/biosql" +DEPEND="${RDEPEND} + dev-perl/Module-Build + test? ( + dev-perl/Data-Stag + dev-perl/Sub-Uplevel + dev-perl/Test-Warn + dev-perl/Test-Exception + virtual/perl-Test-Simple + ) +" +src_prepare() { + export GENTOO_DB_HOSTNAME=localhost + perl-module_src_prepare +} +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} +src_test() { + einfo "Removing bundled test libraries t/lib" + rm -r "${S}/t/lib" || die "Cannot remove t/lib" + + ebegin "Setting up test database" + + local mysqld="${EPREFIX}/usr/sbin/mysqld" + local socket="${T}/mysql.sock" + local pidfile="${T}/mysql.pid" + local datadir="${T}/mysql-data-dir" + local mysql="${EPREFIX}/usr/bin/mysql" + + mkdir -p "${datadir}" || die "Can't make mysql database dir"; + chmod 755 "${datadir}" || die "Can't fix mysql database dir perms"; + + if $mysqld --help | grep -q MariaDB ; then + "${EPREFIX}"/usr/share/mysql/scripts/mysql_install_db \ + --basedir="${EPREFIX}/usr" \ + --datadir="${datadir}" \ + --user=$(whoami) || die "Can't initalize database" + fi + + ${mysqld} --no-defaults --user=$(whoami) --skip-networking \ + --socket="${socket}" \ + --pid-file="${pidfile}" \ + --datadir="${datadir}" & + maxtry=20 + while ! [[ -S "${socket}" || "${maxtry}" -lt 1 ]] ; do + maxtry=$((${maxtry}-1)) + echo -n "." + sleep 1 + done + eend $? + export MYSQL_UNIX_PORT="${socket}" + perl-module_src_test + ebegin "Shutting down mysql test database" + pkill -F "${pidfile}" + eend $? +} diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild new file mode 100644 index 000000000000..e6f0c45958a9 --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-DB +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="test" +RESTRICT="test" +SRC_TEST="do" + +CDEPEND=" + >=sci-biology/bioperl-${PV} + dev-perl/DBD-mysql + dev-perl/DBI + sci-biology/biosql" +DEPEND="${CDEPEND} + dev-perl/Module-Build + test? ( + dev-perl/Data-Stag + dev-perl/Sub-Uplevel + dev-perl/Test-Warn + dev-perl/Test-Exception + virtual/perl-Test-Simple + ) +" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} +src_test() { + einfo "Removing bundled test libraries t/lib" + rm -r "${S}/t/lib" || die "Cannot remove t/lib" + perl-module_src_test +} diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild new file mode 100644 index 000000000000..2575b8c6af71 --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +CDEPEND=">=sci-biology/bioperl-${PV} + dev-perl/DBI + sci-biology/biosql" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-db-${PV}" + +src_configure() { + # This disables tests. TODO: Enable tests + sed -i -e '/biosql_conf();/d' \ + -e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch new file mode 100644 index 000000000000..36698651c7d1 --- /dev/null +++ b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch @@ -0,0 +1,45 @@ +From d689a1473977b0aa368590ba1f913521e4f466c7 Mon Sep 17 00:00:00 2001 +From: Kent Fredric <kentfredric@gmail.com> +Date: Tue, 18 Jul 2017 16:02:26 +1200 +Subject: [PATCH] Allow custom host/port configurations + +--- + Build.PL | 4 ++-- + t/DBTestHarness.pm | 4 ++-- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/Build.PL b/Build.PL +index ecc402e..a61190f 100755 +--- a/Build.PL ++++ b/Build.PL +@@ -97,9 +97,9 @@ sub biosql_conf { + or die "Error: could not write to config file '$config_file'\n"; + + my %config = (driver => $drivers[0], +- host => '127.0.0.1', ++ host => $ENV{GENTOO_DB_HOSTNAME} || '127.0.0.1', + user => 'root', +- port => 3306, ++ port => $ENV{GENTOO_DB_PORT} || undef, + password => '', + dbname => 'bioseqdb', + database => 'biosql', +diff --git a/t/DBTestHarness.pm b/t/DBTestHarness.pm +index b660429..91e0c54 100755 +--- a/t/DBTestHarness.pm ++++ b/t/DBTestHarness.pm +@@ -47,9 +47,9 @@ my $counter=0; + # Default settings as a hash + my $dflt = { + 'driver' => 'mysql', +- 'host' => 'localhost', ++ 'host' => $ENV{GENTOO_DB_HOST} || 'localhost', + 'user' => 'root', +- 'port' => undef, ++ 'port' => $ENV{GENTOO_DB_PORT} || undef, + 'password' => '', + 'schema_sql' => ['../biosql-schema/sql/biosqldb-mysql.sql'], + 'database' => 'biosql', +-- +2.13.1 + diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml new file mode 100644 index 000000000000..09e1cb381b7f --- /dev/null +++ b/sci-biology/bioperl-db/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl-DB</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest new file mode 100644 index 000000000000..f67e3356a393 --- /dev/null +++ b/sci-biology/bioperl-network/Manifest @@ -0,0 +1,6 @@ +DIST BioPerl-Network-1.006900.tar.gz 2198089 SHA256 5b31ab7d048ee8e7bd6ba933f96b904d7ee06b46ab29c00276eca3513a77c32a SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842 WHIRLPOOL 65ff9e2509c0136232b7cff1aa5e8ad55f26241f51e70e6d34f9383c0af4bfdb0c5358b1a69075d480e9e1fdfa19342058fbe33ea4d4a633220ef3a80d6ed984 +EBUILD bioperl-network-1.6.9.ebuild 610 SHA256 dc93700854168aa40031bfe94e80e6d975f47f6e5fac37e0a7ce89b20c46adb3 SHA512 75a872e2925c8d7662caad9e68d490fb1be835ef26038aaf7520765c15ae87b64369d7123715e8182f3ee3a0017a441a45a869e743e6773162831e75b1ebe4c4 WHIRLPOOL 554bcf9bf5b258231573adf5d8afc8ad6b0d748bea00074b7a285ccedc07cd3c5c851f3b1219fe65ab0ddb7231e7b733ead61fd7fd50fd812f0751462504e48c +EBUILD bioperl-network-9999-r1.ebuild 642 SHA256 f379eff4781d05243b7ab092f3ac599d75baa500cb9d056f1f8edd74d3c7f900 SHA512 455ccb0f4b3b426d6930f2efed4771a2538afafe47141defec5532500ea75a2954bf4e71f39ec7a3229821e74dcf1aecdce370c5e05479e4317ebc2553936ab4 WHIRLPOOL 7eb7e90fe9db66cbe4c8c5df30329ab3d0fe97c153b1f6402b9f0a157ac378d8032b69a00cce254b16aeefa0b19f4cabf19cbd75307d4fe326fb161cb3551164 +MISC ChangeLog 2528 SHA256 4589847b8ae0a16d85f9d7e1f4384e5abb1d217a36bb121e3e92d71930850d4b SHA512 cb78e0b6d9922a7c3d0ff081c67ef7ffa165b86a4f2aa2a632d25b14e6ccd6833134ce186b774c49651e73880b6bb6599bff9b5cda377b7e8d1838709785f944 WHIRLPOOL 12dd76ba1d96355ed4907c0298a3e423e820f4dd7ce5d8c05afdafb5c96bf7b350cfeb4911de65dd25f57195ac6215c5ca8075183695a85ca949ed25a69655e6 +MISC ChangeLog-2015 2323 SHA256 c902f57dbd1e62a8d0138e1c881dbe807a073d246085ce096a71093eaf5f1e2d SHA512 9fe2d1a42326a333c406220c1a4360394ac801b06c1dc823b62bd73526420cc1ecad9ec6274cbbdc49048aac46a3da2cc968e6810b519d8a7965fbd109c00e43 WHIRLPOOL 0d730ec28006f081c90576eae34524ea24bfa47e051ad060062ec41c92df1d5941849d0a3e0a6fc2f354f2bae46b52e0e00f3e0dbbc04a68b79ac9104f17c52c +MISC metadata.xml 349 SHA256 35823cecbbe6d4817306fbda6be70259eb44b35dc61ad81cb991cd7b5b4a9aa5 SHA512 dc3b8e26619cb4ff0dffeb79aa91f402a35cb2f673ecfd0bdac9d3667be82c248dcdd246185a006e8b91c9b66157689eaaf8ee464e00c54227c2c78cd9827b63 WHIRLPOOL dad0685cce0f620edd00c400187833f13b2e89e889074c891cef41dbb09ea802f91bc6ea77662cf5730f04eeaff115ca2f6d10e4d51d01588c49999f8ffdeb09 diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild new file mode 100644 index 000000000000..f199589337d9 --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-Network +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="test" +SRC_TEST="do" + +CDEPEND=">=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS" + perl-module_src_install +} diff --git a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild new file mode 100644 index 000000000000..19dc6f7d52e4 --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="test" +SRC_TEST="do" + +CDEPEND=">=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-network-${PV}" + +src_install() { + mydoc="AUTHORS BUGS" + perl-module_src_install +} diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml new file mode 100644 index 000000000000..754b8d123313 --- /dev/null +++ b/sci-biology/bioperl-network/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl-Network</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest new file mode 100644 index 000000000000..af2014cefcc3 --- /dev/null +++ b/sci-biology/bioperl-run/Manifest @@ -0,0 +1,6 @@ +DIST BioPerl-Run-1.006900.tar.gz 14546677 SHA256 6eddca8aae38a139caaa0b28505e2ff3e919e8ed39b7539a662b0145f1f08d96 SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c WHIRLPOOL a671180b3680d94683e771ba661e0f86430814200efcd8df1552dbc3c30228d90ea8be1b47cc36603cbfc6eadacb276414ae6d79e30ec80495fd836eb1732cca +EBUILD bioperl-run-1.6.9.ebuild 931 SHA256 216193a88c247f5a94a8a1fbddf5c84142394e05db0c696528f3704de1ed15b8 SHA512 b512b3fc62208ab6ef1c6f160d43c5e9b8a3f03131398144ec4e4e1ddb1973f45b121220e71724a0c621ff58ea33b5f639cd23dedd62e033f3e78118dde2e94e WHIRLPOOL 59e5583d20d1305d680e7bf99beac19155bb9ea4cd87f5227c616a95f91feb36062a9994073d961e10befdde1157238f8c4689a1a3b25a308337d76936119538 +EBUILD bioperl-run-9999-r1.ebuild 928 SHA256 3dddc8db1c7d8a40ba5de894447187f28bf678fec04362a6a2506b900a688b80 SHA512 42449a6ab99ccd3779899536eb525b6bf029fe477d65e5d8c66958b5803749180c06d068fdc4c06c3de0bbb9987751f6b5886ee446fdec92db5683f8e41a8e4d WHIRLPOOL 6b9b5e13a2af762a7a8c29f02c2ec6c81caeeda4b72265153124d37b9e189121175c0f8d1f4ac459c370a946ff5e8ef63fb7432433617c16c9f78652bdb161f5 +MISC ChangeLog 2714 SHA256 a8deb18bf7045efe57adde6efaa255ea359d1bbe7d7a3b61390723673706d4d8 SHA512 3180ce2c1971714fac7483346234d68c0b54833cb51267abea8072a0ce9afb93758ae2a6cfc8c9e8ba6323b2c0a1f78825ca43ba199847053317bc30d1b585b0 WHIRLPOOL 416604ad2e83fd017fd897bd0a93ae0b08f2893fe6db04bcef34d3e6647c47eeb68bdff7947586e707a49a2fff5e0e20a416fbb666c1df9b96d1aa7c2b0dfc77 +MISC ChangeLog-2015 4922 SHA256 894c5d73973fd308ef87e47c9ec9200d4fa6e69cbaa48add3ec1bbc0da5ac61e SHA512 3810afc32235725f917639aee6a21ad83521d32787efa453d54098c89fac36d04f7573bb8c93d3fd7f02db897382417e17a14cfe3ffa865b6d88d41c7a99dd03 WHIRLPOOL 143823eb2873eaa24a283bfda5a347ada22f018e1a87308a8fc3e502d1b4a929b7d1d0a61d7f9fb705850fec35b1ab6f108c23a2dbfe1f23b936473eef3c11d2 +MISC metadata.xml 345 SHA256 925b0030884af3b8c4a9cb3a539154ca27318dc788b9e1f3d51f0b1511ac9427 SHA512 23370e5fb887d48f37f6ef1d3fa45092fb3b45e111f82488153ce5235bdd7671bed559093927ad92e3c7876f390e385d032fbf9e76a55cb00a0da7fa80bea2ad WHIRLPOOL 9c0136ff7780364d07d2aa08f249cdb07f3723e65dbc957251dbeaaa3c5cc178fbb0712ccbb31e021de12c92b051766a86429781fa7d3c55ea0ecbb3b7c8d46d diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild new file mode 100644 index 000000000000..e5dc816bc78a --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-Run +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl wrapper modules for key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="-minimal test" +#SRC_TEST="do" + +RESTRICT="test" + +CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + dev-perl/File-Sort + )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) + # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D + #find "${D}" -name '*ConfigData*' -print -delete +} diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild new file mode 100644 index 000000000000..2052432904af --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl wrapper modules for key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="-minimal test" +#SRC_TEST="do" + +RESTRICT="test" + +CDEPEND=">=sci-biology/bioperl-${PV} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-run-${PV}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) + # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D + find "${D}" -name '*ConfigData*' -print -delete +} diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml new file mode 100644 index 000000000000..5fccf50862ad --- /dev/null +++ b/sci-biology/bioperl-run/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl-Run</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest new file mode 100644 index 000000000000..d4fd5b9c45c0 --- /dev/null +++ b/sci-biology/bioperl/Manifest @@ -0,0 +1,6 @@ +DIST BioPerl-1.6.901.tar.gz 12284856 SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 WHIRLPOOL feb1f93a617e0135ab84b0eeb36ac986e817ce76ada0f40518090f6a480fbb1047339b33fcd11ccff444f89c4a06c41b5abaab66b662a50f17ae34f9b22d66fd +EBUILD bioperl-1.6.9.ebuild 1544 SHA256 48af54169e933b299b5cbccb8d024c622ce54b16b16c2b81de60eb8a50e30dbf SHA512 2e6167abb3ab729eef114ef9e38955e5d2b5353efaf86f5af16aa00348a661adc5b2297f22c2a77126c7f4f3f08f3db9c0af4210ddb3328653f11b1f5a782744 WHIRLPOOL c44238e73089079e645711b59e2ca75071ed0c92b193fe5990ba2a72d1b06b8c80d85ed73921883a92be04b61144b1f600796e6d210b7477b6bc7af74bc609ba +EBUILD bioperl-9999-r1.ebuild 1793 SHA256 4572481f8dcf47e793219278f5c745861d6142c469e2bc337a703b636674f53b SHA512 25459e6fdeacb6bded0c81a4bbd3a6d85f7cbae973b6f9b8a2ee1a44ab56b5a81556b1c6176e389e57efa660fdb35a6b61c71aca65f90e221bc04a0dda395e5c WHIRLPOOL 2a78b548458705effdc5cdedef1615933643415548ab47d75c7735fb212307378107709a4d47748993ea534b7ec85619bf1f6df4d522a280a206405951297530 +MISC ChangeLog 3082 SHA256 922b31d7106a75064fc95c36bee21e8674e13efa8922d9d48a5c992c822517bf SHA512 b3af13290548dbd7d06a468b1c7cda939861bae04813d69e88f8a7e48ef191757b6315375c25d4e88932cf4a890fd6851f23c97e537f35913262be26fa40ca25 WHIRLPOOL 9f0b7b6dc145e0001cfc628e353f3e7a1f825b6da378bc8a0dc725889cefdd83e33a8095b76c17f03e7475e4d54047130a815eeb20baae530556c2870186980a +MISC ChangeLog-2015 10092 SHA256 c62eae3a76746911bc6ba9682db44cae7205fab5fbde5e04f6ff55c22b5d55c6 SHA512 dc29fc462dc9b6c9d0dfe57c7e594b7d12da79aa12382e0ac738a48c470e0051ecac32b15c1af79d68183798050a2d09ebed07e8bbd78305ffa5cee4a3fba657 WHIRLPOOL 657e7f90335f20d92a4eea80d606464e279a282b85603c12b289e446204d00f6e02aa6b761fac0802a3f95ebd4f5ea38adb7e1a9ec9b1c53e1b16e9a4adb74af +MISC metadata.xml 541 SHA256 83910a66da15199aa7cc29e9fca93cea8bfd8edb96f9efdf549dcf6c8ea3fa2e SHA512 0693aba25e02d3ad67f82c2c77f9987ae06cb6545bb58df2c57f076a22d5c2f6d15c7fdc11b0766748680d53c709c7682b53f866a4f45d7d8a875d1311277e5c WHIRLPOOL b6359f4f497274340afabe6c6e83290c4be0c58b48598216061cc5f81c8a8ba263e2bc408fd2d00a4450bf3750091ad5d01e6321c7843c3cb4d73a993df101de diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild new file mode 100644 index 000000000000..d2519a0d30b6 --- /dev/null +++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +MY_PN=BioPerl +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.6.901 +inherit perl-module + +SUBPROJECTS="+db +network +run" +MIN_PV=$PV + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" + +REQUIRED_USE="minimal? ( !graphviz )" + +CDEPEND=" + dev-perl/libwww-perl + !minimal? ( + dev-perl/Algorithm-Munkres + dev-perl/Array-Compare + dev-perl/YAML + dev-perl/Bio-ASN1-EntrezGene + dev-perl/Clone + dev-perl/Convert-Binary-C + dev-perl/Data-Stag + dev-perl/GD + dev-perl/Graph + >=dev-perl/HTML-Parser-3.60 + dev-perl/List-MoreUtils + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/Set-Scalar + dev-perl/SOAP-Lite + dev-perl/Sort-Naturally + dev-perl/Spreadsheet-ParseExcel + >=virtual/perl-Storable-2.05 + >=dev-perl/SVG-2.26 + >=dev-perl/SVG-Graph-0.01 + dev-perl/URI + >=dev-perl/XML-DOM-XPath-0.13 + dev-perl/XML-Parser + >=dev-perl/XML-SAX-0.15 + dev-perl/XML-Simple + dev-perl/XML-Twig + >=dev-perl/XML-Writer-0.4 + dev-perl/XML-DOM + dev-perl/XML-XPath + ) + graphviz? ( dev-perl/GraphViz ) + sqlite? ( dev-perl/DBD-SQLite )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" +PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} ) + network? ( >=sci-biology/bioperl-network-${MIN_PV} ) + run? ( >=sci-biology/bioperl-run-${MIN_PV} )" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild new file mode 100644 index 000000000000..f166946c008f --- /dev/null +++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit perl-module git-2 + +SUBPROJECTS="+db +network +run" + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/${PN}/${PN}-live.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="-minimal graphviz ${SUBPROJECTS}" + +CDEPEND=" + dev-perl/Data-Stag + dev-perl/libwww-perl + !minimal? ( + dev-perl/Ace + dev-perl/Bio-ASN1-EntrezGene + dev-perl/Spreadsheet-ParseExcel + dev-perl/Spreadsheet-WriteExcel + >=dev-perl/XML-SAX-0.15 + dev-perl/Graph + dev-perl/SOAP-Lite + dev-perl/Array-Compare + dev-perl/SVG + dev-perl/XML-Simple + dev-perl/XML-Parser + dev-perl/XML-Twig + >=dev-perl/HTML-Parser-3.60 + >=dev-perl/XML-Writer-0.4 + dev-perl/Clone + dev-perl/XML-DOM + dev-perl/Set-Scalar + dev-perl/XML-XPath + dev-perl/XML-DOM-XPath + dev-perl/Algorithm-Munkres + dev-perl/Data-Stag + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/Convert-Binary-C + dev-perl/SVG-Graph + ) + graphviz? ( dev-perl/GraphViz )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" +PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) + db? ( >=sci-biology/bioperl-db-${PV} ) + network? ( >=sci-biology/bioperl-network-${PV} ) + run? ( >=sci-biology/bioperl-run-${PV} )" + +S="${WORKDIR}/BioPerl-${PV}" + +src_configure() { + sed -i -e '/add_post_install_script.*symlink_script.pl/d' \ + -e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \ + -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \ + || die + if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml new file mode 100644 index 000000000000..1cd5db0e9619 --- /dev/null +++ b/sci-biology/bioperl/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="run">Install sci-biology/bioperl-run</flag> + <flag name="network">Install sci-biology/bioperl-run</flag> + <flag name="db">Install sci-biology/bioperl-run</flag> + </use> + <upstream> + <remote-id type="cpan">BioPerl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest new file mode 100644 index 000000000000..9219f3e4b869 --- /dev/null +++ b/sci-biology/biopython/Manifest @@ -0,0 +1,5 @@ +DIST biopython-1.68.tar.gz 14445813 SHA256 d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 WHIRLPOOL 9348354d0063efe0f9051f46e3be60540c5df21a43c094d74e64d37279736921d890cd639c904336eb21b2996e9948b8a050017b77569d2333ac80aa5b8bf156 +EBUILD biopython-1.68.ebuild 1645 SHA256 17014ab913a356416b73ae696b7862e0536c47a10b017dd5fe22e049f5dff4a1 SHA512 23418100fa56983329f389e46f1124e3e03eca7614fac6c9465a53be765742e50029060f3c9efbea8ab2eeba02eb1c617e705c26fee65a47d030d0e436b97f03 WHIRLPOOL b308da34762e6ef1845a28f7b84fb629482ecfd84451718c6abeaf3bce71ff2c8b0fdde6142e1184b5d2528b5399358203ff161bc21cfaf0f39d8b874000fea2 +MISC ChangeLog 3520 SHA256 148533b2d48445a82765f8d34118ff94b4967fc09132ea88d9baadc83273f79b SHA512 b032a3a05e2804ebda1b7db5742b2a2ef4021cfb240d74367a0aebd6edb810ae544c5a751459edf190928f6843e13c5833b47b0727761bcc882f67baf225d06f WHIRLPOOL 28d3df06e0eff7838e0d958e7f65e6d99d9bc38c9f96969172815f92937e2cf25cb8ba152a432c19a70839df0f200b22154b8f544cd4c7a972a4d5ecb629b91e +MISC ChangeLog-2015 13216 SHA256 cc9c6b624ea4635f4346a34cf7ba4771364f161175177268e24a646ada9db31d SHA512 197cfe74bd1b98c0580ce07bf30ea23b21a7549a6c365588838468ccd3cebc4f9952370e44e6a9f66f4eac34c0239fe46de60732640c664cd49991c40487f198 WHIRLPOOL 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biology" +HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[$(python_gen_usedep 'python*')] + dev-python/networkx[$(python_gen_usedep 'python*')] + dev-python/numpy[$(python_gen_usedep 'python*')] + dev-python/rdflib[$(python_gen_usedep 'python*')] + dev-python/pygraphviz[$(python_gen_usedep 'python2*')] + dev-python/reportlab[$(python_gen_usedep 'python*')] + dev-python/pydot[$(python_gen_usedep 'python2*')] + " +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) + +python_test() { + distutils_install_for_testing + cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die + cd "${TEST_DIR}"/lib/Tests || die + rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die + ${PYTHON} run_tests.py --offline --verbose || die +} + +python_install_all() { + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED%/}"/usr/share/${PN} || die +} + +pkg_postinst() { + elog "For database support you need to install:" + optfeature "MySQL" dev-python/mysql-python + optfeature "PostGreSQL" dev-python/psycopg + elog + elog "Some applications need extra packages:" + optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss +} diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/biopython/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/bioruby/Manifest b/sci-biology/bioruby/Manifest new file mode 100644 index 000000000000..0404ed685d63 --- /dev/null +++ b/sci-biology/bioruby/Manifest @@ -0,0 +1,8 @@ +AUX bioruby-1.4.3.0001-fix-tests.patch 1082 SHA256 a2347c4e0c731ab24d3054002837de16821b26956e0ffeac97c62b6591c7ca5a SHA512 0a46f8d049521d90993274b52d7bece39464999a4286ac2052a7c8cfb97fe31af7eeadfc8d42c2cbd71f80aca6ac6a778eeb1de7341368ef2ee726444b74752e WHIRLPOOL 05aad8aa4e2a60c5215b6a26ccd942b8fa687a5bce99a0918db6f3a859be961ba131c5a74c3badfede98019a70c793c0153de873aff1d984872383fc4fe3ddc7 +DIST bio-1.5.1.gem 1445376 SHA256 896c19af7e724e038baceae20c00688872b70c69ef966ef3adc42696d001b441 SHA512 822ac6c3d85847193fc1992087abc868e4d1a7cfca82da6ab1830af2927a2a582c3993bc681e129a6aac224ed1cb0b33056d8cc02d3e36d68c9d6a4153c321ca WHIRLPOOL fc8ca3cc508e5d1c95b986cb64eaf28641833498110530a625836117d4a55e9bc01e91da9cd9d71ec40de209e4adb683fff0337260d7b0d8fe30b0659bed94c6 +DIST bioruby-1.4.3.0001.tar.gz 1500656 SHA256 20d6548e1c5977464afd74019693dde9e45a030d48d974db08a7b85c4214fb35 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821 WHIRLPOOL ccb952d4cd3b8700acbf356a0965842b068aa2fb861dfab58e7442e5570ab79604a8be1fb86a9d80d6bc9a8f9dc886daf98cb84fe7298b4f334e0e6be198f9e7 +EBUILD bioruby-1.4.3.0001-r1.ebuild 720 SHA256 2defe33e7f52e6890931b9ef9643b763a9ad6f94d9cfd6f7610419a4fea060e7 SHA512 9a929ffe9e804ce835d0399fad4afa9dd8b0d9d2acfd234d2944168826e05d77e538c1163ad5add74b62433a10319b1b492d91ddd8786ba52dabbf7b27ea2b8f WHIRLPOOL ecfc151b2cf910cea88fea75b3574c02fe7def8b90c8244693a1a71adda0106e3e3d8ce42b0ea6f2d5432806a6ad87356e4d679b62f630385daf7b9e466d7db2 +EBUILD bioruby-1.5.1.ebuild 440 SHA256 273aff24621c87dadbf37ac00f31432f279487cdc9ab80f338909744065d6c0d SHA512 b6812050b69f792b268d9e06e0d72f19d4b7a01d4fcb8fd8aa335ac111359f4585de8f7a55793192c94a7291f2caf0e038668aa5a0a5171b762a3fc04f6d1e2d WHIRLPOOL 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537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild new file mode 100644 index 000000000000..de7ff26eeb4b --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +USE_RUBY="ruby21 ruby22" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://bioruby.org/" +SRC_URI="http://${PN}.org/archive/${P}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="amd64 ~ppc x86" + +ruby_add_rdepend "dev-ruby/libxml" + +PATCHES=( "${FILESDIR}"/${P}-fix-tests.patch ) + +each_ruby_configure() { + ${RUBY} setup.rb config || die +} + +each_ruby_compile() { + ${RUBY} setup.rb setup || die +} + +each_ruby_install() { + ${RUBY} setup.rb install --prefix="${D}" || die +} + +each_ruby_test() { + ${RUBY} -rubygems test/runner.rb || die +} diff --git a/sci-biology/bioruby/bioruby-1.5.1.ebuild b/sci-biology/bioruby/bioruby-1.5.1.ebuild new file mode 100644 index 000000000000..f5e558c7ff33 --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.5.1.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +USE_RUBY="ruby21 ruby22 ruby23" + +RUBY_FAKEGEM_NAME="bio" + +RUBY_FAKEGEM_EXTRAINSTALL="etc" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://bioruby.org/" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~ppc ~x86" + +ruby_add_rdepend "dev-ruby/libxml" diff --git a/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch new file mode 100644 index 000000000000..71c4ca27104a --- /dev/null +++ b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch @@ -0,0 +1,29 @@ +From edda65b8fb32c2eee6b0652074981c31aa68b0eb Mon Sep 17 00:00:00 2001 +From: Naohisa Goto <ng@bioruby.org> +Date: Fri, 23 Aug 2013 23:51:59 +0900 +Subject: [PATCH] Test bug fix: Read test file with binary mode to avoid + encoding error + + * Test bug fix: Read test file with binary mode to avoid string encoding + error. Thanks to nieder (github.com/nieder) who reports the bug. + (https://github.com/bioruby/bioruby/issues/84) +--- + test/unit/bio/db/test_phyloxml.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/unit/bio/db/test_phyloxml.rb b/test/unit/bio/db/test_phyloxml.rb +index 0744c64..c24278d 100644 +--- a/test/unit/bio/db/test_phyloxml.rb ++++ b/test/unit/bio/db/test_phyloxml.rb +@@ -100,7 +100,7 @@ def test_open_with_block + end + + def test_new +- str = File.read(TestPhyloXMLData.example_xml) ++ str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read } + assert_instance_of(Bio::PhyloXML::Parser, + phyloxml = Bio::PhyloXML::Parser.new(str)) + common_test_next_tree(phyloxml) +-- +1.8.4 + diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-biology/bioruby/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/biosql/Manifest b/sci-biology/biosql/Manifest new file mode 100644 index 000000000000..adcb409dbba8 --- /dev/null +++ b/sci-biology/biosql/Manifest @@ -0,0 +1,5 @@ +DIST biosql-1.0.1.tar.bz2 253516 SHA256 3604ceaf6f3e42a11613b49577b7c68f04d9e094cca4e5d932359c815fc9ad01 SHA512 2e1fef6ab9b4386f146910937700f9108f8ef266161b7adfbbc52c0011eebc84716637c897a01a399ff39b066ff0a5905ba3fa27e7b41f53a87baf58d5b32695 WHIRLPOOL 3f29a647dc991dd59840aa681df8d5664a15ca5b83a72bb23926517dd8e7734c2db8b07e1f426c73a99fa72ef13e3fd3255c67eeb09ae11afc6804bfaa8a5d54 +EBUILD biosql-1.0.1-r1.ebuild 989 SHA256 ca3ac50d2fec3c37a05e724c4ae7bc836227e01d7ece5b52dac1f634b9de9932 SHA512 874448ac12a4e0331ec7b7b5ce8843928f92a6b42987975380715d39f7d0fc5c0cf688c4a596963ae5b008b55367fab3db317a8d17a19230d113e4d8e142c37f WHIRLPOOL d92e69a119ed8a1f1e17d79e354a7a2a6558a6192950b589acc34e0d5f06b9a51231d41a4aab3f940b633668a4422a1b8dad22b38b38f05551e43df9db99b3ec +MISC ChangeLog 2427 SHA256 9e245904d449f003463811df37ad7a13dcb52c8a6f267c3d206a8f4903aa4525 SHA512 282237f1fe33f8d73270970e4d20ae5fbbb731d78a0195a7d439e1c72937da38ab242553af7a0056bebe6bad6f6803a0c9ff6f87db7220ffd2575b3ca112c00e WHIRLPOOL cbb0d8828adfd028ab16aa5410bc07b4c3e2ce6971cce89942d897cd4f6265b70c2840d79400dd43ef05f99fe447e98c0bc861f0685b5e17ea7cd955e55f34c9 +MISC ChangeLog-2015 820 SHA256 d6640bdb2894832c6ac2711f92f9b0692d358da83480f27983417fee81383d38 SHA512 2692437c36287fb01616e34c7e75b91cc62a635b9a5dca3fc5de9096a1a5fc14f5b251a7e5d7c14d4638c32b7b65417431b0cb465c00a7c147f181e04a83d473 WHIRLPOOL 8802950e9882d07bb853e2353b00c416a0f531800d54a086fec51949cf8e22fdd7cf6a9ac8b2144d3dbe9d0012cbe890d7e6c8552c2e0dba2040efd664264a77 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/biosql/biosql-1.0.1-r1.ebuild b/sci-biology/biosql/biosql-1.0.1-r1.ebuild new file mode 100644 index 000000000000..6508d6a3a2e8 --- /dev/null +++ b/sci-biology/biosql/biosql-1.0.1-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="A generic bioinformatics relational database model" +HOMEPAGE="http://www.biosql.org/" +SRC_URI="http://biosql.org/DIST/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="mysql postgres" + +# WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL) + +DEPEND=" + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg )" +RDEPEND=" + ${DEPEND} + dev-lang/perl" + +src_install() { + insinto /usr/share/${PN} + doins -r sql scripts/. + + dodoc Changes README Release.txt doc/*.pdf + + docinto biopython + dodoc doc/{README,schema-overview.txt,biopython/{cor6_6.gb,*.pdf}} + docompress -x /usr/share/doc/${PF}/biopython + + docinto html + dodoc doc/{biopython/,}*.htm* +} + +pkg_postinst() { + elog + elog "Please read the BioSQL schema installation instructions in" + elog "${EROOT%/}/usr/share/doc/${PF} to begin using the schema." + elog +} diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/biosql/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest new file mode 100644 index 000000000000..f8a3a9fbea98 --- /dev/null +++ b/sci-biology/blat/Manifest @@ -0,0 +1,6 @@ +AUX blat-34-fix-build-system.patch 5249 SHA256 03d563305183f9b40dbc6073f7ccfaaafc0240afcd7ed70da8638c43b7e5a2eb SHA512 1c4b592ef1b45ea19d84a798f4d526c43851bf8545d4a9aaaa8842c76eff1e0e31a179d1cd914e44f67c1d5ac709b97a73a5b7e66fa680f6531efe50b6dc6246 WHIRLPOOL b878a41fba2dda93fd0dbb32e5cea634aa7bd879d9b9094b130281b98c7a953a057df512d58eda36437a78248831b7e5bde8b07fd8807144fe158efcab0b8108 +DIST blatSrc34.zip 2142975 SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8 WHIRLPOOL eace9c1befa8b3b019f0adc6047429fcede604c380ae52522efadb69dea2de4fb7878e961895abe7eebfcdc9a4c40ba16bb9479f13b16fde7f720933ebb7f323 +EBUILD blat-34-r2.ebuild 807 SHA256 e839e891e5bd99dc37fc667ec154c7a168eb31341860d15112dbff2fef24594b SHA512 451b189b505331cd7c045fc19982d55d11673afdfa8f0f9bd2b57cd23097c5a066afe477d973a0f30e1a47a8d1893abc552ef8ccc5f59ce9f3a66e0ceedc94b2 WHIRLPOOL 0b72a2d14033b09e692f8ce1d9391dc0e8f6433057b54810f1827625e811e122374a95fe7f88e1e23ecc1dda83329ba034e5395f6c99ffe4101949facc17f970 +MISC ChangeLog 2485 SHA256 a8b3f5d2e60062ccbc233f2b11ea21b4bbf3869c1cbe9e16c656438493f1cdca SHA512 4c4025e50e831076ab02eb8ea2e11fd1e0800ea6c5d50df6065c914dd72c9c3e09f10b55f520f2c24cef8a50383f694cbed6a53521209892460e3d074415b274 WHIRLPOOL 5e15c6c391137f039ea202277f9361b05b8dc447fa7709d7f7c10a9054b1c0ea2f30ab400fee42dbb1ff26e19324a2f2a6349b0a7a8b8db2f1940ea2cf32cb89 +MISC ChangeLog-2015 831 SHA256 727ef35729a38580c3b0ee1094570a011bd5ef617a4a532d780523f8bc03f7de SHA512 702193bebc1a967f6a4c9f6f72e380cfeec2ffc19885a367c1356b7fbf4eac4ed8acb20da023a5c2e38f6e5cf5ffa0e72a362c80b98c3ead24d1a44625a49c97 WHIRLPOOL 831cb7a9b8e69891f0922250c7ee68b65c9f4416e6e5c38c93a819f34b45371606dccc2cf0ea96c29cfda3d08f7951d4d45b5fe97f87f890f73e3c1fb5539fc6 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild new file mode 100644 index 000000000000..e10bc367a311 --- /dev/null +++ b/sci-biology/blat/blat-34-r2.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_PN=${PN}Src + +DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" +HOMEPAGE="http://www.cse.ucsc.edu/~kent/" +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" + +LICENSE="blat" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="app-arch/unzip" + +S=${WORKDIR}/${MY_PN} + +PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch ) + +src_compile() { + tc-export AR CC + + export HOME="${S}" + export MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + + mkdir -p bin/${MACHTYPE} || die + default +} + +src_install() { + export MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + + dobin bin/${MACHTYPE}/* +} diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch new file mode 100644 index 000000000000..361149cc1211 --- /dev/null +++ b/sci-biology/blat/files/blat-34-fix-build-system.patch @@ -0,0 +1,207 @@ +--- a/blat/makefile ++++ b/blat/makefile +@@ -7,7 +7,7 @@ + O = blat.o + + blat: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/blat${EXE} + + all: +--- a/gfClient/makefile ++++ b/gfClient/makefile +@@ -8,5 +8,5 @@ + X = gfClient + + gfClient: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} +--- a/gfServer/makefile ++++ b/gfServer/makefile +@@ -8,7 +8,7 @@ + X = gfServer + + gfServer: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} + + test: +--- a/hg/pslPretty/makefile ++++ b/hg/pslPretty/makefile +@@ -8,7 +8,7 @@ + O = pslPretty.o + + pslPretty: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L + + test:: testRna testDnax + +--- a/hg/pslReps/makefile ++++ b/hg/pslReps/makefile +@@ -9,7 +9,7 @@ + O = pslReps.o + + pslReps: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L + + lib: + cd ../../lib && ${MAKE} +--- a/hg/pslSort/makefile ++++ b/hg/pslSort/makefile +@@ -8,7 +8,7 @@ + O = pslSort.o + + pslSort: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L + + + lib: +--- a/inc/common.mk ++++ b/inc/common.mk +@@ -1,20 +1,15 @@ +-CC=gcc +-ifeq (${COPT},) +- COPT=-O +-endif +-CFLAGS= + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} + HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type + HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc + + # Stronger warning checks, and warnings-->errors, for libraries and CGIs: + ifeq (darwin,$(findstring darwin,${OSTYPE})) +- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable ++ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable + else + ifeq (solaris,$(findstring solaris,${OSTYPE})) + HG_WARN_ERR = -DJK_WARN -Wall + else +- HG_WARN_ERR = -DJK_WARN -Wall -Werror ++ HG_WARN_ERR = -DJK_WARN -Wall + endif + endif + # Apply the stronger checks to all code on our development machine: +@@ -37,7 +32,7 @@ + endif + MKDIR=mkdir -p + ifeq (${STRIP},) +- STRIP=strip ++ STRIP=true + endif + CVS=cvs + +--- a/jkOwnLib/makefile ++++ b/jkOwnLib/makefile +@@ -9,7 +9,7 @@ + T = ../lib/$(MACHTYPE)/jkOwnLib.a + + $(T): $(O) ../lib/$(MACHTYPE) +- ar rcus $(T) $(O) ++ $(AR) rcus $(T) $(O) + + ../lib/$(MACHTYPE): + mkdir ../lib/$(MACHTYPE) +--- a/lib/makefile ++++ b/lib/makefile +@@ -32,7 +32,7 @@ + + + $(MACHTYPE)/jkweb.a: $(O) $(MACHTYPE) +- ar rcus $(MACHTYPE)/jkweb.a $(O) ++ $(AR) rcus $(MACHTYPE)/jkweb.a $(O) + + $(MACHTYPE): + mkdir $(MACHTYPE) +--- a/makefile ++++ b/makefile +@@ -1,18 +1,18 @@ + all: +- cd lib && ${MAKE} +- cd jkOwnLib && ${MAKE} +- cd blat && $(MAKE) +- cd gfClient && $(MAKE) +- cd gfServer && $(MAKE) +- cd hg/pslPretty && $(MAKE) +- cd hg/pslReps && $(MAKE) +- cd hg/pslSort && $(MAKE) +- cd utils/nibFrag && $(MAKE) +- cd utils/faToNib && $(MAKE) +- cd utils/faToTwoBit && $(MAKE) +- cd utils/twoBitToFa && $(MAKE) +- cd utils/twoBitInfo && $(MAKE) +- cd webBlat && $(MAKE) ++ $(MAKE) -C lib ++ $(MAKE) -C jkOwnLib ++ $(MAKE) -C blat ++ $(MAKE) -C gfClient ++ $(MAKE) -C gfServer ++ $(MAKE) -C hg/pslPretty ++ $(MAKE) -C hg/pslReps ++ $(MAKE) -C hg/pslSort ++ $(MAKE) -C utils/nibFrag ++ $(MAKE) -C utils/faToNib ++ $(MAKE) -C utils/faToTwoBit ++ $(MAKE) -C utils/twoBitToFa ++ $(MAKE) -C utils/twoBitInfo ++ $(MAKE) -C webBlat + + clean: + rm -f */*.o */*/*.o +--- a/utils/faToNib/makefile ++++ b/utils/faToNib/makefile +@@ -8,4 +8,4 @@ + O = faToNib.o + + faToNib: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L +--- a/utils/faToTwoBit/makefile ++++ b/utils/faToTwoBit/makefile +@@ -7,7 +7,7 @@ + O = faToTwoBit.o + + faToTwoBit: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/faToTwoBit${EXE} + + clean: +--- a/utils/nibFrag/makefile ++++ b/utils/nibFrag/makefile +@@ -4,7 +4,7 @@ + O = nibFrag.o + + nibFrag: $(O) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a + + + +--- a/utils/twoBitInfo/makefile ++++ b/utils/twoBitInfo/makefile +@@ -7,7 +7,7 @@ + O = twoBitInfo.o + + twoBitInfo: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/twoBitInfo${EXE} + + clean: +--- a/utils/twoBitToFa/makefile ++++ b/utils/twoBitToFa/makefile +@@ -8,7 +8,7 @@ + O = twoBitToFa.o + + twoBitToFa: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L + #${STRIP} ${BINDIR}/twoBitToFa${EXE} + + clean: diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/blat/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest new file mode 100644 index 000000000000..0a75c9164e33 --- /dev/null +++ b/sci-biology/blossoc/Manifest @@ -0,0 +1,7 @@ +AUX blossoc-1.4.0-fix-build-system.patch 8380 SHA256 ea66141979346a032ede2fd9653a71e59ce580ff9a89f4b022f2aff01b35315a SHA512 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75bd413cdca1ddbdf5c645653d5fb1684aa0ff1252a0b9baf9aaba391e6831e731ab6566fb5b81c52a7bb84e01db9a84f08d21f599997dd52bc8802d21d72865 WHIRLPOOL 49aba78c0b6e6e4b7117256d5306d8657ba657f68438f8c72e60d7679733609f417a7ebaaaf0df2a3ec988bac436a3930c90d4f1d10da724d26546fd3fbb1924 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild new file mode 100644 index 000000000000..9fd1189e025a --- /dev/null +++ b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="A linkage disequilibrium association mapping tool" +HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/" +SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-libs/gsl:= + dev-libs/boost:= + sci-biology/snpfile" +DEPEND=" + ${RDEPEND} + >=sys-devel/autoconf-archive-2016.09.16 + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${PN}-1.4.0-gcc43.patch + "${FILESDIR}"/${PN}-1.4.0-fix-build-system.patch +) + +src_prepare() { + default + mv configure.{in,ac} || die + rm m4/ax_boost.m4 || die + eautoreconf +} diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch new file mode 100644 index 000000000000..21234cc3cfb3 --- /dev/null +++ b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch @@ -0,0 +1,256 @@ +* Modernise Autoconf code +* Use pkg-config for finding GSL +* Use latest archvie macros to find Boost +* Compile tests only when running make check + +--- a/configure.in ++++ b/configure.in +@@ -1,6 +1,6 @@ + AC_INIT(blossoc, 1.4.0, mailund@birc.au.dk) + AM_INIT_AUTOMAKE +-AM_CONFIG_HEADER(config.hh) ++AC_CONFIG_HEADERS([config.hh]) + + AC_PROG_CXX + AC_PROG_INSTALL +@@ -12,74 +12,16 @@ + fi + AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix]) + +-AC_CHECK_LIB(m, sin, dnl FOUND, DO NOTHING +-, dnl NOT FOUND +-AC_ERROR([[ +-************************************************************************ +-************************************************************************ +-Didn't find the math library (-lm) -- I won't even guess about what is +-wrong on this machine... +-************************************************************************ +-************************************************************************ +-]]) +-) +- +-AX_BOOST([1.33.1],, +-AC_ERROR([[ +-************************************************************************ +-************************************************************************ +-The Boost library was not found on this system. We use this library +-extensively, and cannot proceed without it. You can obtain it from +-<http://www.boost.org>. +-************************************************************************ +-************************************************************************ +-]]) +-) +- +- +-AC_CHECK_LIB(gslcblas, cblas_dsdot, dnl FOUND, DO NOTHING +-, dnl NOT FOUND +-AC_ERROR([[ +-************************************************************************ +-************************************************************************ +-The GNU Scientific Library (GSL) was not found. This library is +-needed for some of the numerical calculations used for scoring the +-significance of local genealogies and can be obtained at +-<http://www.gnu.org/software/gsl/>. +-************************************************************************ +-************************************************************************ +-]]) +-) +- +-AC_CHECK_LIB(gsl, gsl_cdf_chisq_Q, dnl FOUND, DO NOTHING +-, dnl NOT FOUND +-AC_ERROR([[ +-************************************************************************ +-************************************************************************ +-The GNU Scientific Library (GSL) was not found. This library is +-needed for some of the numerical calculations used for scoring the +-significance of local genealogies and can be obtained at +-<http://www.gnu.org/software/gsl/>. +-************************************************************************ +-************************************************************************ +-]]) +-) +- +-AC_CHECK_LIB(snpfile, main, dnl main isn't there, but this avoids namespaces +-dnl FOUND +-, +-dnl NOT FOUND +-AC_ERROR([[ +-************************************************************************ +-************************************************************************ +-The SNPFile library was not found. This library is needed for data +-representation and can be obtained at +-<http://www.birc.au.dk/~mailund/SNPFile/>. +-************************************************************************ +-************************************************************************ +-]]) +-) +- ++AC_SEARCH_LIBS([sin], [m], [], [ ++ AC_MSG_ERROR([unable to find the sin() function]) ++]) ++ ++PKG_CHECK_MODULES([GSL], [gsl]) ++ ++AX_BOOST_BASE([1.33.1]) ++AX_BOOST_PROGRAM_OPTIONS ++AX_BOOST_SERIALIZATION ++AX_BOOST_SIGNALS + + AC_OUTPUT([ + Makefile +--- a/Makefile.am ++++ b/Makefile.am +@@ -3,9 +3,6 @@ + AM_CXXFLAGS += -Wall + AM_CXXFLAGS += $(BOOST_CPPFLAGS) + +-# for testing +-AM_CXXFLAGS += -g -O0 #-lefence +- + # for coverage testing + #AM_CXXFLAGS += -O3 -fexpensive-optimizations -g -fprofile-arcs -ftest-coverage + +@@ -15,11 +12,11 @@ + # for production + #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG + +-noinst_PROGRAMS = ++check_PROGRAMS = ++noinst_PROGRAMS = + TESTS = + EXTRA_DIST = + +-TESTS += first_test.sh + EXTRA_DIST += first_test.sh + + man_MANS = blossoc.1 snpfile_blossoc.1 blossoc_regions.1 blossoc_trees.1 +@@ -37,20 +34,20 @@ + noinst_PROGRAMS += snpfile_iblossoc #ditto + noinst_PROGRAMS += fast_snpfile_iblossoc + +-noinst_PROGRAMS += matrix_test +-TESTS += matrix_test +-noinst_PROGRAMS += incompatibility_test tree_test tree_builder_test +-TESTS += incompatibility_test tree_test tree_builder_test ++check_PROGRAMS += matrix_test ++TESTS += matrix_test ++check_PROGRAMS += incompatibility_test tree_test tree_builder_test ++TESTS += incompatibility_test tree_test tree_builder_test + EXTRA_DIST += testdata/CF/cf-positions.txt + EXTRA_DIST += testdata/CF/cf-haplotypes.txt + EXTRA_DIST += testdata/interaction/positions.txt + EXTRA_DIST += testdata/interaction/haplotypes.txt +-noinst_PROGRAMS += score_test io_test +-TESTS += score_test io_test +-noinst_PROGRAMS += incompatible_regress_test +-TESTS += incompatible_regress_test +-noinst_PROGRAMS += genotype_score_test +-TESTS += genotype_score_test.sh ++check_PROGRAMS += score_test io_test ++TESTS += score_test io_test ++check_PROGRAMS += incompatible_regress_test ++TESTS += incompatible_regress_test ++check_PROGRAMS += genotype_score_test ++TESTS += genotype_score_test.sh + EXTRA_DIST += genotype_score_test.sh + EXTRA_DIST += genotype_score_test.expected + TESTS += interactions_regression_test.sh +@@ -120,6 +117,7 @@ + + + blossoc_regions_LDADD = ++blossoc_regions_LDADD += -lsnpfile + blossoc_regions_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + blossoc_regions_SOURCES = + blossoc_regions_SOURCES += incompatibility.hh incompatibility.cc +@@ -129,6 +127,7 @@ + blossoc_regions_SOURCES += regions.cc + + blossoc_trees_LDADD = ++blossoc_trees_LDADD += -lsnpfile + blossoc_trees_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + blossoc_trees_SOURCES = + blossoc_trees_SOURCES += matrix_utils.hh matrix_utils.cc +@@ -142,6 +141,8 @@ + + + blossoc_LDADD = ++blossoc_LDADD += -lsnpfile ++blossoc_LDADD += $(GSL_LIBS) + blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + blossoc_SOURCES = + blossoc_SOURCES += tree.hh tree.cc +@@ -158,6 +159,8 @@ + blossoc_SOURCES += blossoc.cc + + snpfile_blossoc_LDADD = ++snpfile_blossoc_LDADD += -lsnpfile ++snpfile_blossoc_LDADD += $(GSL_LIBS) + snpfile_blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + snpfile_blossoc_LDADD += $(BOOST_SERIALIZATION_LIB) + snpfile_blossoc_LDADD += $(BOOST_SIGNALS_LIB) +@@ -176,6 +179,8 @@ + snpfile_blossoc_SOURCES += snpfile_blossoc.cc + + iblossoc_LDADD = ++iblossoc_LDADD += -lsnpfile ++iblossoc_LDADD += $(GSL_LIBS) + iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + iblossoc_SOURCES = + iblossoc_SOURCES += tree.hh tree.cc +@@ -191,6 +196,8 @@ + iblossoc_SOURCES += interactions.cc + + low_mem_iblossoc_LDADD = ++low_mem_iblossoc_LDADD += -lsnpfile ++low_mem_iblossoc_LDADD += $(GSL_LIBS) + low_mem_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + low_mem_iblossoc_SOURCES = + low_mem_iblossoc_SOURCES += tree.hh tree.cc +@@ -206,6 +213,8 @@ + low_mem_iblossoc_SOURCES += low_mem_interactions.cc + + snpfile_iblossoc_LDADD = ++snpfile_iblossoc_LDADD += -lsnpfile ++snpfile_iblossoc_LDADD += $(GSL_LIBS) + snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB) + snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB) +@@ -223,6 +232,8 @@ + snpfile_iblossoc_SOURCES += snpfile_interactions.cc + + fast_snpfile_iblossoc_LDADD = ++fast_snpfile_iblossoc_LDADD += -lsnpfile ++fast_snpfile_iblossoc_LDADD += $(GSL_LIBS) + fast_snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) + fast_snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB) + fast_snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB) +@@ -239,6 +250,28 @@ + fast_snpfile_iblossoc_SOURCES += io.hh io.cc + fast_snpfile_iblossoc_SOURCES += fast_snpfile_interactions.cc + ++matrix_test_LDADD = ++matrix_test_LDADD += -lsnpfile ++ ++incompatibility_test_LDADD = ++incompatibility_test_LDADD += -lsnpfile ++ ++tree_builder_test_LDADD = ++tree_builder_test_LDADD += -lsnpfile ++ ++score_test_LDADD = ++score_test_LDADD += -lsnpfile ++score_test_LDADD += $(GSL_LIBS) ++ ++io_test_LDADD = ++io_test_LDADD += -lsnpfile ++ ++incompatible_regress_test_LDADD = ++incompatible_regress_test_LDADD += -lsnpfile ++ ++genotype_score_test_LDADD = ++genotype_score_test_LDADD += -lsnpfile ++genotype_score_test_LDADD += $(GSL_LIBS) + + + # include GUI in source distributions... diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch new file mode 100644 index 000000000000..64b5fe46e30e --- /dev/null +++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch @@ -0,0 +1,15 @@ +Fixes build with >=GCC-4.3 + +http://bugs.gentoo.org/show_bug.cgi?id=292949 + +Patch written by Sebastian Luther <SebastianLuther@gmx.de> +--- a/pph.cc ++++ b/pph.cc +@@ -23,6 +23,7 @@ + */ + + #include "pph.hh" ++#include <cstdio> + #include <cmath> + #include <snpfile/matrix.hh> + using namespace BiRC::SNPFile; diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/blossoc/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest new file mode 100644 index 000000000000..155be157845f --- /dev/null +++ b/sci-biology/bowtie/Manifest @@ -0,0 +1,19 @@ +AUX bowtie-1.1.2-_ContextLss-1.1-1.4.patch 601 SHA256 3fc2e55806824558c12e7d3ae3f4be77f9897f222e1de06c3ab39dff74fa7ad7 SHA512 e39ec6323cc6fee49a6ecf3565066d9cb8f8001af2701de292025f268d57dcfa3d4c35f3e2aed56b7e3835a955e5bfb595214ac232309fcc46c6d51f83cd9f2e WHIRLPOOL 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1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301 WHIRLPOOL 32a4afad7cafe525f0da2c13cc632be5b061863562a7591291699d5d49b45aa831a15ca721e998fcc69acd1107a92495a38fc8826cf73af0ed83b85f52efdadd diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild new file mode 100644 index 000000000000..d8b607f870fc --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +IUSE="examples +tbb" + +RDEPEND="tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + sci-biology/seqan:1.4 + app-arch/unzip" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +PATCHES=( + "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" + "${FILESDIR}/${P}-fix-setBegin-call.patch" + "${FILESDIR}/${P}-seqan-popcount.patch" + "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" + "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" + "${FILESDIR}/${P}-spelling.patch" + "${FILESDIR}/${P}-tbb-tinythread-missing.patch" + "${FILESDIR}/${P}-unbundle-seqan.patch" +) + +src_prepare() { + default + + # remove bundled libraries, use system seqan 1.4 + rm -rf SeqAn-1.1/ third_party/ || die + + # innocuous non-security flags, prevent log pollution + append-cxxflags \ + -Wno-unused-local-typedefs \ + -Wno-unused-but-set-variable \ + -Wno-unused-variable +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild new file mode 100644 index 000000000000..1ada8a0fdc2b --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.1.2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="1" +KEYWORDS="amd64 x86 ~x64-macos" + +IUSE="examples +tbb" + +DEPEND="app-arch/unzip + tbb? ( dev-cpp/tbb )" +RDEPEND="" + +DOCS=( AUTHORS NEWS TUTORIAL doc/README ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_prepare() { + # always include tinythread.cpp + epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch" +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN} ${PN}-* + + exeinto /usr/libexec/${PN} + doexe scripts/* + + newman MANUAL ${PN}.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN} + doins -r genomes indexes + fi +} diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild new file mode 100644 index 000000000000..29826473a3b3 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.6.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="amd64 x86" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl" +DEPEND="${RDEPEND} + app-arch/unzip + tbb? ( dev-cpp/tbb )" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN}2 ${PN}2-* + + exeinto /usr/libexec/${PN}2 + doexe scripts/* + + newman MANUAL ${PN}2.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +} diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild new file mode 100644 index 000000000000..0bacb8ca25d7 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.9.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="examples cpu_flags_x86_sse2 +tbb" + +RDEPEND="dev-lang/perl + tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) +PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" ) + +pkg_pretend() { + if ! use cpu_flags_x86_sse2 ; then + eerror "This package requires a CPU supporting the SSE2 instruction set." + die "SSE2 support missing" + fi +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" \ + WITH_TBB="$(usex tbb 1 0)" +} + +src_install() { + dobin ${PN}2 ${PN}2-* + + exeinto /usr/libexec/${PN}2 + doexe scripts/* + + newman MANUAL ${PN}2.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +} diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch new file mode 100644 index 000000000000..78b9c01a0462 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch @@ -0,0 +1,17 @@ +Description: Change class name of _Context_LSS + New version 1.4 of SeQan uses a different name of the class. +Forwarded: no +Author: Gert Wollny <gw.fossdev@gmail.com> +Last-Update: 2014-100-06 + +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -856,7 +856,7 @@ void DifferenceCoverSample<TStr>::build( + { + Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); + VMSG_NL(" Invoking Larsson-Sadakane on ranks"); +- _Context_LSS<TIndexOff> c; ++ ContextLss_<TIndexOff> c; + c.suffixsort( + (TIndexOff*)begin(_isaPrime, Standard()), + (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch new file mode 100644 index 000000000000..af7f7f61cd5e --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch @@ -0,0 +1,42 @@ +Description: Proper type-casting in using seqan::_setBegin(). + Required by newer versions of GCC. +Forwarded: no +Author: Ognyan Kulev <ogi@debian.org> +Last-Update: 2013-04-18 + +--- a/pat.h ++++ b/pat.h +@@ -82,20 +82,20 @@ struct ReadBuf { + ~ReadBuf() { + clearAll(); reset(); + // Prevent seqan from trying to free buffers +- _setBegin(patFw, NULL); +- _setBegin(patRc, NULL); +- _setBegin(qual, NULL); +- _setBegin(patFwRev, NULL); +- _setBegin(patRcRev, NULL); +- _setBegin(qualRev, NULL); +- _setBegin(name, NULL); ++ _setBegin(patFw, (Dna5*)NULL); ++ _setBegin(patRc, (Dna5*)NULL); ++ _setBegin(qual, (char*)NULL); ++ _setBegin(patFwRev, (Dna5*)NULL); ++ _setBegin(patRcRev, (Dna5*)NULL); ++ _setBegin(qualRev, (char*)NULL); ++ _setBegin(name, (char*)NULL); + for(int j = 0; j < 3; j++) { +- _setBegin(altPatFw[j], NULL); +- _setBegin(altPatFwRev[j], NULL); +- _setBegin(altPatRc[j], NULL); +- _setBegin(altPatRcRev[j], NULL); +- _setBegin(altQual[j], NULL); +- _setBegin(altQualRev[j], NULL); ++ _setBegin(altPatFw[j], (Dna5*)NULL); ++ _setBegin(altPatFwRev[j], (Dna5*)NULL); ++ _setBegin(altPatRc[j], (Dna5*)NULL); ++ _setBegin(altPatRcRev[j], (Dna5*)NULL); ++ _setBegin(altQual[j], (char*)NULL); ++ _setBegin(altQualRev[j], (char*)NULL); + } + } + diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch new file mode 100644 index 000000000000..52cb4f496521 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch @@ -0,0 +1,24 @@ +Description: Use SeqAn 1.4's seqan::popCount() function instead of own function +Author: Ognyan Kulev <ogi@debian.org> +Last-Update: 2014-03-08 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -476,6 +476,8 @@ static String<T> getDeltaMap(T v, const + return amap; + } + ++// Debian: Use seqan::popCount ++#if 0 + /** + * Return population count (count of all bits set to 1) of i. + */ +@@ -488,6 +490,7 @@ static unsigned int popCount(T i) { + } + return cnt; + } ++#endif + + /** + * Calculate log-base-2 of i diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch new file mode 100644 index 000000000000..171f9bab8fae --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch @@ -0,0 +1,382 @@ +Description: Renamed ChunkPool class to bowtieChunkPool. + SeqAn has a class with the same name and fatal name collision happens. +Forwarded: no +Author: Ognyan Kulev <ogi@debian.org> +Last-Update: 2013-04-18 + +--- a/aligner.h ++++ b/aligner.h +@@ -337,7 +337,7 @@ public: + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt = NULL, + AlignerMetrics *metrics = NULL) : + Aligner(true, rangeMode), +@@ -544,7 +544,7 @@ protected: + bool quiet_; // don't print informational/warning info + + const int maxBts_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + int *btCnt_; + AlignerMetrics *metrics_; + }; +@@ -585,7 +585,7 @@ public: + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt) : + Aligner(true, rangeMode), + refs_(refs), +@@ -1358,7 +1358,7 @@ protected: + bool quiet_; + + int maxBts_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + int *btCnt_; + + // Range-finding state for first mate +@@ -1482,7 +1482,7 @@ public: + bool verbose, + bool quiet, + int maxBts, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + int *btCnt) : + Aligner(true, rangeMode), + refs_(refs), +@@ -2035,7 +2035,7 @@ protected: + TDriver* driver_; + + // Pool for distributing chunks of best-first path descriptor memory +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + + bool verbose_; + bool quiet_; +--- a/aligner_0mm.h ++++ b/aligner_0mm.h +@@ -32,7 +32,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -124,7 +124,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + bool maqPenalty_; +@@ -164,7 +164,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -366,7 +366,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + const bool reportSe_; +--- a/aligner_1mm.h ++++ b/aligner_1mm.h +@@ -32,7 +32,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -161,7 +161,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + const bool maqPenalty_; +@@ -201,7 +201,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -478,7 +478,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + const bool reportSe_; +--- a/aligner_23mm.h ++++ b/aligner_23mm.h +@@ -33,7 +33,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -231,7 +231,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + const bool maqPenalty_; +@@ -273,7 +273,7 @@ public: + RangeCache *cacheFw, + RangeCache *cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -675,7 +675,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + const bool reportSe_; +--- a/aligner_seed_mm.h ++++ b/aligner_seed_mm.h +@@ -37,7 +37,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool maqPenalty, +@@ -554,7 +554,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + bool strandFix_; +@@ -598,7 +598,7 @@ public: + RangeCache* cacheFw, + RangeCache* cacheBw, + uint32_t cacheLimit, +- ChunkPool *pool, ++ bowtieChunkPool *pool, + BitPairReference* refs, + vector<String<Dna5> >& os, + bool reportSe, +@@ -1375,7 +1375,7 @@ private: + RangeCache *cacheFw_; + RangeCache *cacheBw_; + const uint32_t cacheLimit_; +- ChunkPool *pool_; ++ bowtieChunkPool *pool_; + BitPairReference* refs_; + vector<String<Dna5> >& os_; + const bool reportSe_; +--- a/ebwt_search.cpp ++++ b/ebwt_search.cpp +@@ -111,7 +111,7 @@ static bool strandFix; // attempt to fi + static bool randomizeQuals; // randomize quality values + static bool stats; // print performance stats + static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread +-static int chunkSz; // size of single chunk disbursed by ChunkPool ++static int chunkSz; // size of single chunk disbursed by bowtieChunkPool + static bool chunkVerbose; // have chunk allocator output status messages? + static bool recal; + static int recalMaxCycle; +@@ -223,7 +223,7 @@ static void resetOptions() { + randomizeQuals = false; // randomize quality values + stats = false; // print performance stats + chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread +- chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB) ++ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB) + chunkVerbose = false; // have chunk allocator output status messages? + recal = false; + recalMaxCycle = 64; +@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); + +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + UnpairedExactAlignerV1Factory alSEfact( + ebwt, + NULL, +@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat + // Global initialization + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + + Unpaired1mmAlignerV1Factory alSEfact( + ebwtFw, +@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); + +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + Unpaired23mmAlignerV1Factory alSEfact( + ebwtFw, + &ebwtBw, +@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt + // Global initialization + PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); + HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); +- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); ++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); + + AlignerMetrics *metrics = NULL; + if(stats) { +--- a/ebwt_search_backtrack.h ++++ b/ebwt_search_backtrack.h +@@ -2724,7 +2724,7 @@ public: + bool verbose, + bool quiet, + bool mate1, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt) : + SingleRangeSourceDriver<EbwtRangeSource>( + params, rs, fw, sink, sinkPt, os, verbose, +@@ -2927,7 +2927,7 @@ public: + bool verbose, + bool quiet, + bool mate1, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt = NULL) : + params_(params), + rs_(rs), +@@ -2986,7 +2986,7 @@ protected: + bool verbose_; + bool quiet_; + bool mate1_; +- ChunkPool* pool_; ++ bowtieChunkPool* pool_; + int *btCnt_; + }; + +--- a/pool.h ++++ b/pool.h +@@ -19,13 +19,13 @@ + * is set at construction time. Heap memory is only allocated at + * construction and deallocated at destruction. + */ +-class ChunkPool { ++class bowtieChunkPool { + public: + /** + * Initialize a new pool with an initial size of about 'bytes' + * bytes. Exit with an error message if we can't allocate it. + */ +- ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : ++ bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : + verbose(verbose_), patid(0), pool_(NULL), cur_(0), + chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz), + bits_(lim_), exhaustCrash_(false), +@@ -38,7 +38,7 @@ public: + } + } catch(std::bad_alloc& e) { + ThreadSafe _ts(&gLock); +- std::cerr << "Error: Could not allocate ChunkPool of " ++ std::cerr << "Error: Could not allocate bowtieChunkPool of " + << totSz << " bytes" << std::endl; + exhausted(); + throw 1; // Exit if we haven't already +@@ -48,7 +48,7 @@ public: + /** + * Delete all the pools. + */ +- ~ChunkPool() { ++ ~bowtieChunkPool() { + if(pool_ != NULL) delete[] pool_; + } + +@@ -189,7 +189,7 @@ public: + * Initialize a new pool with an initial size of about 'bytes' + * bytes. Exit with an error message if we can't allocate it. + */ +- AllocOnlyPool(ChunkPool* pool, const char *name) : ++ AllocOnlyPool(bowtieChunkPool* pool, const char *name) : + pool_(pool), name_(name), curPool_(0), cur_(0) + { + assert(pool != NULL); +@@ -388,7 +388,7 @@ protected: + lastCurInPool_.pop_back(); + } + +- ChunkPool* pool_; ++ bowtieChunkPool* pool_; + const char *name_; + std::vector<T*> pools_; /// the memory pools + uint32_t curPool_; /// pool we're current allocating from +--- a/range_source.h ++++ b/range_source.h +@@ -1388,7 +1388,7 @@ class PathManager { + + public: + +- PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : ++ PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : + branchQ_(verbose, quiet), + cpool(cpool_), + bpool(cpool, "branch"), +@@ -1637,7 +1637,7 @@ protected: + + public: + +- ChunkPool *cpool; // pool for generic chunks of memory ++ bowtieChunkPool *cpool; // pool for generic chunks of memory + AllocOnlyPool<Branch> bpool; // pool for allocating Branches + AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates + AllocOnlyPool<Edit> epool; // pool for allocating Edits +@@ -1811,7 +1811,7 @@ public: + bool quiet, + bool mate1, + uint32_t minCostAdjustment, +- ChunkPool* pool, ++ bowtieChunkPool* pool, + int *btCnt) : + RangeSourceDriver<TRangeSource>(true, minCostAdjustment), + len_(0), mate1_(mate1), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch new file mode 100644 index 000000000000..38664aeee989 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch @@ -0,0 +1,85 @@ +Description: Renamed seqan::fill function calls to use seqan::resize. + SeqAn 1.3 renamed seqan::fill() to seqan::resize(). + SeqAn ticket: http://trac.seqan.de/ticket/77 +Forwarded: no +Author: Ognyan Kulev <ogi@debian.org> +Last-Update: 2014-08-13 + +--- a/blockwise_sa.h ++++ b/blockwise_sa.h +@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS + try { + // Allocate and initialize containers for holding bucket + // sizes and representatives. +- fill(bucketSzs, numBuckets, 0, Exact()); +- fill(bucketReps, numBuckets, OFF_MASK, Exact()); ++ resize(bucketSzs, numBuckets, 0, Exact()); ++ resize(bucketReps, numBuckets, OFF_MASK, Exact()); + } catch(bad_alloc &e) { + if(this->_passMemExc) { + throw e; // rethrow immediately +@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl + // Not the last bucket + assert_lt(_cur, length(_sampleSuffs)); + hi = _sampleSuffs[_cur]; +- fill(zHi, _dcV, 0, Exact()); ++ resize(zHi, _dcV, 0, Exact()); + assert_eq(zHi[0], 0); + calcZ(t, hi, zHi, this->verbose(), this->sanityCheck()); + } +@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl + assert_gt(_cur, 0); + assert_leq(_cur, length(_sampleSuffs)); + lo = _sampleSuffs[_cur-1]; +- fill(zLo, _dcV, 0, Exact()); ++ resize(zLo, _dcV, 0, Exact()); + assert_gt(_dcV, 3); + assert_eq(zLo[0], 0); + calcZ(t, lo, zLo, this->verbose(), this->sanityCheck()); +--- a/diff_sample.h ++++ b/diff_sample.h +@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const + // Declare anchor-map-related items + String<T> amap; + size_t amapEnts = 1; +- fill(amap, v, 0xffffffff, Exact()); ++ resize(amap, v, 0xffffffff, Exact()); + amap[0] = 0; + // Print out difference cover (and optionally calculate + // anchor map) +@@ -532,7 +532,7 @@ public: + assert_gt(_d, 0); + assert_eq(1, popCount(_v)); // must be power of 2 + // Build map from d's to idx's +- fill(_dInv, _v, 0xffffffff, Exact()); ++ resize(_dInv, _v, 0xffffffff, Exact()); + uint32_t lim = (uint32_t)length(_ds); + for(uint32_t i = 0; i < lim; i++) { + _dInv[_ds[i]] = i; +@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil + VMSG_NL(" Doing sanity check"); + TIndexOffU added = 0; + String<TIndexOffU> sorted; +- fill(sorted, length(_isaPrime), OFF_MASK, Exact()); ++ resize(sorted, length(_isaPrime), OFF_MASK, Exact()); + for(size_t di = 0; di < this->d(); di++) { + uint32_t d = _ds[di]; + size_t i = 0; +@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS + assert_eq(length(_doffs), d+1); + // Size sPrime appropriately + reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS +- fill(sPrime, sPrimeSz, OFF_MASK, Exact()); ++ resize(sPrime, sPrimeSz, OFF_MASK, Exact()); + // Slot suffixes from text into sPrime according to the mu + // mapping; where the mapping would leave a blank, insert a 0 + TIndexOffU added = 0; +@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build( + // arrays back into sPrime. + VMSG_NL(" Allocating rank array"); + reserve(_isaPrime, length(sPrime)+1, Exact()); +- fill(_isaPrime, length(sPrime), OFF_MASK, Exact()); ++ resize(_isaPrime, length(sPrime), OFF_MASK, Exact()); + assert_gt(length(_isaPrime), 0); + { + Timer timer(cout, " Ranking v-sort output time: ", this->verbose()); diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch new file mode 100644 index 000000000000..ff484dfa3ebb --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch @@ -0,0 +1,48 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Thu, 01 Oct 2015 09:47:23 +0200 +Description: Fix spelling + +--- a/MANUAL ++++ b/MANUAL +@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie + actually wrapper scripts that call binary programs as appropriate. The + wrappers shield users from having to distinguish between "small" and + "large" index formats, discussed briefly in the following section. The +-appropiate index type is selected based on the input size. ++appropriate index type is selected based on the input size. + + It is recommended that you always run the bowtie wrappers and not run + the binaries directly. +--- a/MANUAL.markdown ++++ b/MANUAL.markdown +@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie + actually wrapper scripts that call binary programs as appropriate. The + wrappers shield users from having to distinguish between "small" and + "large" index formats, discussed briefly in the following section. The +-appropiate index type is selected based on the input size. ++appropriate index type is selected based on the input size. + + It is recommended that you always run the bowtie wrappers and not run + the binaries directly. +--- a/doc/manual.html ++++ b/doc/manual.html +@@ -201,7 +201,7 @@ T2302111203131231130300111123220 + <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p> + <p>Note that SOLiD-generated read files can have "orphaned" mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click "NGS: QC and manipulation", then "SOLiD-to-FASTQ" in the left-hand sidebar).</p> + <h2 id="wrapper-scripts">Wrapper scripts</h2> +-<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p> ++<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p> + <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p> + <h2 id="small-and-large-indexes">Small and large indexes</h2> + <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a "large" index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p> +--- a/ref_read.cpp ++++ b/ref_read.cpp +@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in, + << "reference into smaller chunks and index each independently." << endl; + #else + cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl +- << "build a large index instead using the appropiate options." << endl; ++ << "build a large index instead using the appropriate options." << endl; + #endif + throw 1; + } diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch new file mode 100644 index 000000000000..bc0f1d09557d --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch @@ -0,0 +1,18 @@ +Fixes missing tinythread.cpp when using TBB: + +ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()' + +--- bowtie-1.1.2/Makefile ++++ bowtie-1.1.2/Makefile +@@ -106,10 +106,7 @@ + endif + + OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ +- edit.cpp ebwt.cpp +-ifneq (1,$(WITH_TBB)) +- OTHER_CPPS += tinythread.cpp +-endif ++ edit.cpp ebwt.cpp tinythread.cpp + + SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \ + log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \ diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch new file mode 100644 index 000000000000..54391ae415a3 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch @@ -0,0 +1,27 @@ +Description: Use Debian packaged SeqAn library instead of copy in upstream source +Author: Andreas Tille <tille@debian.org> +Date: 2011-01-30 +Last-Update: 2013-04-18 +Reviewed-by: Ognyan Kulev <ogi@debian.org> + +--- a/Makefile ++++ b/Makefile +@@ -5,9 +5,7 @@ + prefix = /usr/local + bindir = $(prefix)/bin + +-SEQAN_DIR = SeqAn-1.1 +-SEQAN_INC = -I $(SEQAN_DIR) +-INC = $(SEQAN_INC) -I third_party ++INC = `pkg-config --cflags seqan-1.4` + CPP = g++ + CXX = $(CPP) + CC = gcc +@@ -168,7 +166,6 @@ + $(wildcard genomes/NC_008253.fna) \ + $(wildcard reads/e_coli_1000.*) \ + $(wildcard reads/e_coli_1000_*) \ +- SeqAn-1.1 \ + bowtie \ + bowtie-build \ + bowtie-inspect \ diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch new file mode 100644 index 000000000000..cd2a67b6a52b --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch @@ -0,0 +1,29 @@ +Fix building with C++14, which errors out due to differing semantics between C++98 +and C++14 with regards to allowing destructors to throw exceptions. +See also: https://bugs.gentoo.org/show_bug.cgi?id=593966 + +--- a/blockwise_sa.h ++++ b/blockwise_sa.h +@@ -87,7 +87,11 @@ + _logger(__logger) + { } + +- virtual ~BlockwiseSA() { } ++ virtual ~BlockwiseSA() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ { } + + /** + * Get the next suffix; compute the next bucket if necessary. +@@ -216,6 +220,9 @@ + { _randomSrc.init(__seed); reset(); } + + ~KarkkainenBlockwiseSA() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + #ifdef WITH_TBB + tbb_grp.wait(); diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml new file mode 100644 index 000000000000..71e8d3bb8e0f --- /dev/null +++ b/sci-biology/bowtie/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> + <use> + <flag name="tbb">Enables building bowtie with the Intel + Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This + flag is recommended.</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest new file mode 100644 index 000000000000..266fd9dce775 --- /dev/null +++ b/sci-biology/bwa/Manifest @@ -0,0 +1,6 @@ +AUX bwa-0.7.15-Makefile.patch 933 SHA256 58b08ded78471266c0b7bfc6042bc52100b38c5c72a4091a1d9391ee9569ea5c SHA512 d76d6aac355b2ad52d3aa1ca59defc33017cfbdcec96939db4807acf7f35d6bcd4e21728998fb0fd3633742cfd9edaa7b62ab1eaff26829296967fefdbc185b4 WHIRLPOOL ab34cbed56aa60c940b5b4949eaed488ba0e01b24d43976e8706759e2f55bbd8a9a5c407571c9bfe08e3f443e7b1e099b9537d216cc4b1c4583ed5ce9c9499f3 +DIST bwa-0.7.16a.tar.bz2 190773 SHA256 8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d WHIRLPOOL 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+DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" +HOMEPAGE="https://bio-bwa.sourceforge.net/" +SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +RDEPEND="dev-lang/perl" + +PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch ) +DOCS=( NEWS.md README-alt.md README.md ) + +src_configure() { + tc-export CC AR +} + +src_install() { + dobin bwa + + exeinto /usr/libexec/${PN} + doexe qualfa2fq.pl xa2multi.pl + + einstalldocs + doman bwa.1 +} diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch new file mode 100644 index 000000000000..39b437a02897 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch @@ -0,0 +1,27 @@ +--- bwa-0.7.13/Makefile ++++ bwa-0.7.13/Makefile +@@ -1,8 +1,8 @@ +-CC= gcc ++CC?= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS?= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o + AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -26,10 +26,10 @@ + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml new file mode 100644 index 000000000000..ceb43ead2a3f --- /dev/null +++ b/sci-biology/bwa/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest new file mode 100644 index 000000000000..2f50b126b920 --- /dev/null +++ b/sci-biology/cd-hit/Manifest @@ -0,0 +1,7 @@ +AUX cd-hit-4.6.6-fix-build-system.patch 4006 SHA256 49944712f599aa023086f825bc56f9e4b3c629c2c28da6203ae3e379fab73aed SHA512 84aadb9967ad65d04127468edb161b8725a5b1468586320eb89d4b4f5f97ad7b60da9728fa1088ecf4aff179a6bda36675add9a255631cf9359c991b61451c6d WHIRLPOOL 674e127461403a449b7789009a25688b8a76fc63d5161cc7c51e1b0c08d39d510982aafa65ca81a5c75d12cab8ad4d5c6a8050e3c89d5e5274213c6cfb5ad3d9 +AUX cd-hit-4.6.6-fix-perl-shebangs.patch 4909 SHA256 94a650eda4f8beecf894eb216dea44ebcc507757cd143b59ced94e2cb779168f SHA512 3ded78d991ee922761a3a7395b4d422ff29c6fe1c0657b61ad74bc6f9253c7dc82414f8d71cfffae37cac192e96ab03f711257d3091cdd0c9444202bdf5967f5 WHIRLPOOL 95baf2dedea0f9f32c14631490b650279d1ea6afc4fede2196301add1c81beb753f89a15e99195c98e044fdd6b91ef8b4706008fb7b7c015775f0305aadf7009 +DIST cd-hit-4.6.6.tar.gz 1152570 SHA256 97946f8ae62c3efa20ad4c527b8ea22200cf1b75c9941fb14de2bdaf1d6910f1 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 WHIRLPOOL 4ee404e34a9c22aef0b809568aa1a7cefcd8d08e4a8c97d1c65b7692ae14b0567e5cc446054083219b56e89895117f69f786e6183f6c67d03d1f8404f7ba9632 +EBUILD cd-hit-4.6.6.ebuild 997 SHA256 a3a6f4ae0e93e513905a55018ef1fc54006807ca42854c5464e21aab69fbd747 SHA512 fe17e01fc04944df9b86b98dc73a4be2f14300938e3e926f56c952eddad62caf846f0051a7c3a66dbca3132f3a79a8bc21d7a43206bd6d9d784b24c94c3204b8 WHIRLPOOL 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691c92d76f2bdb3ed31a802fb1003905942abfb7cef3c1d08848e69cc819082e82540217f7fc79ad39d11a2d43c45b845617bd8ad1282a7bde505ed8616b5364 WHIRLPOOL 9e0529fb4354c4e392b6985165e75d780bde0a3f3d9ce1cb40191ff752e771e62855328e24cf61746d44f690542bb1f833f5be690bb5cd1def64e5ac765371f6 diff --git a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.6.ebuild new file mode 100644 index 000000000000..ebe345f15245 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.6.6.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +RELDATE="2016-0711" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="https://github.com/weizhongli/cdhit/releases/download/V${PV}/${RELEASE}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="openmp" + +RDEPEND="dev-lang/perl" + +S="${WORKDIR}"/${RELEASE} + +PATCHES=( + "${FILESDIR}"/${PN}-4.6.6-fix-perl-shebangs.patch + "${FILESDIR}"/${PN}-4.6.6-fix-build-system.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_compile() { + tc-export CXX + emake openmp=$(usex openmp) +} + +src_install() { + dodir /usr/bin + PREFIX="${EPREFIX}"/usr/bin default + + dodoc doc/*.pdf +} diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch new file mode 100644 index 000000000000..c668d5c6154e --- /dev/null +++ b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch @@ -0,0 +1,122 @@ +Fix build system, in order to honour user variables + +--- a/makefile ++++ b/makefile +@@ -1,7 +1,4 @@ +- +-CC = g++ -Wall -ggdb +-CC = g++ -pg +-CC = g++ ++CXX ?= g++ + + # without OpenMP + +@@ -9,35 +6,19 @@ + # in command line: + # make openmp=yes + ifeq ($(openmp),no) +- CCFLAGS = -DNO_OPENMP +-else +- CCFLAGS = -fopenmp +-endif +- +-# support debugging +-# in command line: +-# make debug=yes +-# make openmp=yes debug=yes +-ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++ my_CPPFLAGS = -DNO_OPENMP + else +-CCFLAGS += -O2 ++ my_CXXFLAGS = -fopenmp + endif + + ifdef MAX_SEQ +-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ) ++my_CPPFLAGS += -DMAX_SEQ=$(MAX_SEQ) + endif + +-#LDFLAGS = -static -o +-LDFLAGS += -o +- + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 + +-# Propagate hardening flags +-CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS) +- + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< + + all: $(PROGS) + +@@ -47,52 +28,52 @@ + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div + + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454 + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-div.c++ -c + + cdhit-454.o: cdhit-454.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-454.c++ -c ++ $(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-454.c++ -c + + PREFIX ?= /usr/local/bin + + install: + for prog in $(PROGS); do \ +- install -m 0755 $$prog $(PREFIX); \ ++ install -m 0755 $$prog $(DESTDIR)$(PREFIX); \ + done +- install -m 0755 *.pl $(PREFIX); ++ install -m 0755 *.pl $(DESTDIR)$(PREFIX); diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch new file mode 100644 index 000000000000..3784296f2e94 --- /dev/null +++ b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch @@ -0,0 +1,219 @@ +Make perl shebangs more Prefix friendly +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/cd-hit-2d-para.pl ++++ b/cd-hit-2d-para.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # ============================================================================= + # CD-HIT + # http://cd-hit.org/ +--- a/cd-hit-div.pl ++++ b/cd-hit-div.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #not like cd-hit-div, this script do not sort input + #or throw away seq +--- a/cd-hit-para.pl ++++ b/cd-hit-para.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # ============================================================================= + # CD-HIT + # http://cd-hit.org/ +--- a/clstr2tree.pl ++++ b/clstr2tree.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $clstr = shift; + $fr = shift; # for nr80.clstr $fr = 0.8 +--- a/clstr2txt.pl ++++ b/clstr2txt.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $no = 0; + my $clstr_no = ""; +--- a/clstr2xml.pl ++++ b/clstr2xml.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...] + #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results +--- a/clstr_cut.pl ++++ b/clstr_cut.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #keep only top $no proteins in cluster + +--- a/clstr_merge_noorder.pl ++++ b/clstr_merge_noorder.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # order of clusters don't need to be the same + # but then I have to read everything into memory +--- a/clstr_merge.pl ++++ b/clstr_merge.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # the order of clusters need to be identical + my ($master_clstr, @clstr) = @ARGV; +--- a/clstr_quality_eval_by_link.pl ++++ b/clstr_quality_eval_by_link.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + ## calculate the sensitivity and specificity of clusters + ## if the input fasta file has pre-defined classification term +--- a/clstr_quality_eval.pl ++++ b/clstr_quality_eval.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + ## calculate the sensitivity and specificity of clusters + ## if the input fasta file has pre-defined classification term +--- a/clstr_reduce.pl ++++ b/clstr_reduce.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + + $file90 = shift; +--- a/clstr_renumber.pl ++++ b/clstr_renumber.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + $no = 0; + while($ll=<>){ + if ($ll =~ /^>Cluster (\d+)/) { +--- a/clstr_rep.pl ++++ b/clstr_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $rep = ""; + $no = 0; +--- a/clstr_reps_faa_rev.pl ++++ b/clstr_reps_faa_rev.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # output single fasta file + # for each cluster output at least $cutoff seqs + +--- a/clstr_rev.pl ++++ b/clstr_rev.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # if nr90 from nr100 and + # nr80 from nr90, so I have nr90.clstr and nr80.clstr + # but, in nr80.clstr, some gi numbers whose from nr100 are there +--- a/clstr_select.pl ++++ b/clstr_select.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #my $by = shift; + my $min; +--- a/clstr_select_rep.pl ++++ b/clstr_select_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #my $by = shift; + my $min; +--- a/clstr_size_histogram.pl ++++ b/clstr_size_histogram.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n"; +--- a/clstr_size_stat.pl ++++ b/clstr_size_stat.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_size_stat.pl clstr_file\n"; +--- a/clstr_sort_by.pl ++++ b/clstr_sort_by.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $sort_by_what = shift; + $sort_by_what = "no" unless $sort_by_what; +--- a/clstr_sort_prot_by.pl ++++ b/clstr_sort_prot_by.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $sort_by = shift; + $sort_by = "len" unless ($sort_by); +--- a/clstr_sql_tbl.pl ++++ b/clstr_sql_tbl.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n"; +--- a/clstr_sql_tbl_sort.pl ++++ b/clstr_sql_tbl_sort.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n"; +--- a/make_multi_seq.pl ++++ b/make_multi_seq.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #note you have to use "-d 0" in the cd-hit run + #note you better to use "-g 1" in the cd-hit run +--- a/plot_2d.pl ++++ b/plot_2d.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Image::Magick; + +--- a/plot_len1.pl ++++ b/plot_len1.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $file90 = shift; + $segs = shift; diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml new file mode 100644 index 000000000000..1f3b075216dd --- /dev/null +++ b/sci-biology/cd-hit/metadata.xml @@ -0,0 +1,27 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> +CD-HIT is a very widely used program for clustering and comparing large sets +of protein or nucleotide sequences. CD-HIT is very fast and can handle +extremely large databases. CD-HIT helps to significantly reduce the +computational and manual efforts in many sequence analysis tasks and aids in +understanding the data structure and correct the bias within a dataset. +The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, +CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT +(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a +user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 +datasets and identifies the sequences in db2 that are similar to db1 above +a threshold. CD-HIT-454 is a program to identify natural and artificial +duplicates from pyrosequencing reads. The usage of other programs and +scripts can be found in CD-HIT user's guide. + </longdescription> + <upstream> + <remote-id type="google-code">cdhit</remote-id> + <remote-id type="github">weizhongli/cdhit</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest new file mode 100644 index 000000000000..7c07314a8c9d --- /dev/null +++ b/sci-biology/clustal-omega/Manifest @@ -0,0 +1,5 @@ +DIST clustal-omega-1.2.4.tar.gz 1170516 SHA256 8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee SHA512 b31514c30b412d731ee22c9020156b65a6a6cbc6fd51edc195d17b560935184bc070feeb58964c54df9eecdefb00e5a21ce859cb0ea69d92917f6bd8e93b819e WHIRLPOOL 86fa6e6f4db128b122abeee470a7c1b0150e64f38d58c6ba620b4b9afd65d91f55d6971fef99b0dfd10ccdc550da1d195eec9a91cdde271947e7a703ca2384d3 +EBUILD clustal-omega-1.2.4.ebuild 649 SHA256 0d5de21a69cd4630618e2bf0be42ca349a715ac17a1b866a1bcc51cb8d348974 SHA512 61ce83c18a97f09dc0750a2da7179aece9c788eb2792fac799a343e219d11f11d7a60980f791313b0963a7aed720d076e55e05c6134155be07e61e18b382c6d8 WHIRLPOOL ee39b39d2ed5f6ec025089678f9bcbca8e62d0094547749e5edeaf6990daa6a12c59681729d9315b8427c90ddfaaad8ac321da50b4a612c7b4c3533542c87b2b +MISC ChangeLog 3785 SHA256 a842dc01b391baa838981038dd87c7b73d8a0f63600db8d7f90bc1ff527b2fd5 SHA512 df80f6697c3bfe68c3ddac0eb11d2dbee49139febac56e98d91f027069f9317cffcb47c4f1c4004c63c8e8b1e19fdf49805f77a1a82edd73a3772f0e94cfba6b WHIRLPOOL 754f631df983677b42244ad7ddb3f475dd74c0f3cdbb6532f31179034d15cf77c5326adee64616d35c03986403b6e6f86d2c850f258e264a86c554fdb05fb4cb +MISC ChangeLog-2015 983 SHA256 9bf682d936740ca31893c01086365cef2438a6b6179f00fae9cb724067e2774e SHA512 d07bfee9607202f8a18d60eb8e47f4d4d5a37321dbd6d9062f9c4eb40cec4c30ff22213a4509ef0881d3575d4fa98d3d9feb7f02d31c4291e08d8ba32c1738a7 WHIRLPOOL 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+HOMEPAGE="http://www.clustal.org/omega/" +SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="static-libs" + +DEPEND="dev-libs/argtable" +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e "s:-O3::g" \ + -i configure.ac || die + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) +} + +src_install() { + default + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/clustal-omega/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest new file mode 100644 index 000000000000..62795800b403 --- /dev/null +++ b/sci-biology/clustalw-mpi/Manifest @@ -0,0 +1,6 @@ +AUX 0.13-gentoo.patch 596 SHA256 10eb9b964fd565833542075a470f70cb4b5624f436b661f442d6951bcf6ebc4a SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8 WHIRLPOOL ec786caa4e73a6a51c643bd756f3f8f6b1dc837c05d57b3fddaddffb52c1b378d00ab48af96992a5c4093874effaa90133e14a1d6e87f7e970a309e246341aa3 +DIST clustalw-mpi-0.13.tar.gz 154911 SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845 SHA512 e0008accb6c07584dc5ad1b953e0c668fad43ca3a86d88dbcf50fbfa858870131e4db005cc87b46f5268cd0795e9a2ce01326d8318d66b694a92b85e6f9635df WHIRLPOOL 850e1f8daff5aeede4bc47779bafa7f331017b854c2f0926fb31b6c40aaf79fb5f8e7605bddee5a9d52043313b578bf1f4e14f060c387ee1ec6e65170fd9fcd7 +EBUILD clustalw-mpi-0.13-r2.ebuild 962 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algorithm" +HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php" +SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="mpi_njtree static_pairalign" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) + +src_prepare() { + default + + if use mpi_njtree; then + sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ + die "Failed to configure MPI code for NJ trees" + fi + + if use static_pairalign; then + sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ + die "Failed to configure static scheduling for pair alignments" + fi +} + +src_install() { + dobin ${PN} + newdoc README.${PN} README +} diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch new file mode 100644 index 000000000000..6e36061cbb39 --- /dev/null +++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch @@ -0,0 +1,23 @@ + Makefile | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index f2107ce..835232b 100644 +--- a/Makefile ++++ b/Makefile +@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE + PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN + #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN + +-CFLAGS = -c -O3 ++CFLAGS += -c + #CFLAGS = -c -O3 -funroll-all-loops +-LFLAGS = -lm ++LIBS = -lm + + clustalw-mpi: $(OBJECTS) +- $(CC) -o $@ $(OBJECTS) $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml new file mode 100644 index 000000000000..8ab4494152c8 --- /dev/null +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> +</maintainer> +<use> + <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing + neighbor-joining trees</flag> + <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling + for pair alignments</flag> +</use> +</pkgmetadata> diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest new file mode 100644 index 000000000000..e4ef57230a9b --- /dev/null +++ b/sci-biology/clustalw/Manifest @@ -0,0 +1,8 @@ +AUX 1.83-as-needed.patch 388 SHA256 e33a1f6f3db1013c3dbd7f35c0dbf0a3665e23d1e2bcad58aaffef046139beda SHA512 1f66a0b539f9101a52b4117d0369294f706a048464d1908ae457def27d33ace0e5c5f9ba507f82a1406bb78ff51896ac6bb76cb03dfe8ff6bbb8ed182dc0f5ea WHIRLPOOL 9c0ca960b32d97b3a7c0f7da468db566c14122b945659c7c36b2cb5c56201373fcf3890654f3371f69d6c188a3131aecd05ce5fc0b98578f331c52cd73164dff +DIST clustalw-2.1.tar.gz 350761 SHA256 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+inherit toolchain-funcs + +DESCRIPTION="General purpose multiple alignment program for DNA and proteins" +HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz" + +LICENSE="clustalw" +SLOT="1" +KEYWORDS="alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" + +S="${WORKDIR}"/${PN}${PV} + +PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) + +src_prepare() { + default + + sed \ + -e "/^CC/s:cc:$(tc-getCC):g" \ + -i makefile || die + sed \ + -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \ + -i clustalw.c || die +} + +src_install() { + dobin clustalw + dodoc README clustalv.doc clustalw{.doc,.ms,_help} +} diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r1.ebuild new file mode 100644 index 000000000000..0b46aeb5bfd4 --- /dev/null +++ b/sci-biology/clustalw/clustalw-2.1-r1.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="General purpose multiple alignment program for DNA and proteins" +HOMEPAGE="http://www.clustal.org/" +SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-3" +SLOT="2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" + +src_install() { + default + rmdir "${ED%/}"/usr/share/aclocal || die +} diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch new file mode 100644 index 000000000000..9bb35b43f24a --- /dev/null +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -0,0 +1,17 @@ +--- a/makefile ++++ b/makefile +@@ -11,11 +11,11 @@ + HEADERS = general.h clustalw.h + + CC = cc +-CFLAGS = -c -O +-LFLAGS = -O -lm ++CFLAGS += -c ++LIBS = -lm + + clustalw : $(OBJECTS) amenu.o clustalw.o +- $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/clustalw/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest new file mode 100644 index 000000000000..0f69514f9a9d --- /dev/null +++ b/sci-biology/clustalx/Manifest @@ -0,0 +1,7 @@ +DIST clustalx-2.1.tar.gz 341649 SHA256 e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 WHIRLPOOL 6cbe8dcf2be3a535e8ac0ef0b9b476d4429a80bd94b394c0194f46ed039f9ac2b97b0ec2ed680838a0973b3187b2dbc90285733657975e03288b9840ba3d6b15 +DIST clustalx.png.xz 74808 SHA256 7d333fd7e96ebc5709ec061e6be4123aba764a6127133cc8df5452f62e0d1cf3 SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a WHIRLPOOL 7d48b4be3ec61d3bd3017a0c0dbf0c3d3970b338cc1050a9c4173d06d268996a733c4a19202fba13e2cd640b72f02ecc9013198a821791edd820f16b5371d234 +EBUILD clustalx-2.1-r1.ebuild 1093 SHA256 b4f39abd38f9ebbc9a4c178a6ec6837eb99d4a6a74d9844d28a7fbeefdd193bb SHA512 997c71482dff6f73841ba912904b9ea34992ffd9dc90466e233017857a93c11a2f930ff242bfc0b1309bedbf4e6be2556bf26efa9a9f7dfe83d0e96abc06e8a0 WHIRLPOOL 95803878825a337224afc5262ee6a2549f1458433065509afb10548a6d578256ce1c0d62cf13a72bbcf33a9e5670bfbdd25d3a3831f313817b9e08c50c4544e7 +EBUILD clustalx-2.1-r2.ebuild 1225 SHA256 bd6017020c3dadd734c715ce3a84ff53e7b42757d3e8276b4553d7e764cc33b0 SHA512 6d0d46521bc2511dca32363e7faf6ff550de74f6e6fcf22f0d3ebd7cbe0f10884dbdb52fcfcba034b4185419d2109663bf1e589d072937b6bbc012fe5ad5c250 WHIRLPOOL 2003f17749c8a87a215fbe05559b1786b40b506ebbed6ccc55298469e9aa7d907156f6c681ee991b8aa6d7517f50c9bd6e70d1f4a830d125ba8b38439b21a926 +MISC ChangeLog 2435 SHA256 b33fcdca9b59ad94c7d48e3dab398f739247e3eb2ba919fb961c12612de3f2cc SHA512 5a7fbb5e2f10c495d2c04222a4e194b5e739b03bfd97fff85f604975ddbabb628d2dfe7b9fce774f480d4b517a455a4da30daaf63b6152bef1b51d44638f643a WHIRLPOOL f95f113d6410eea87655d67ad7a7e29593459bbbccb0bc265195d12fd8d0769c885888d21f71c3766a6875b333c14dcd90288262ea694a5629a6a9b1ee8c13ea +MISC ChangeLog-2015 5285 SHA256 488232e993e1a5d379fd4335175226efa20b7a19d120c84aa2b23406409abf15 SHA512 07c2a77c647da4bedf95a9f353de9353f90f51b838379a0eef96d401ecd073688283991a200cf1d0b93e726db3d38dd60c1def58b1ba132a1ccf65efad328e7f WHIRLPOOL 984359f1319c3a55cf2cf722c026e65405d749287b5367b9379a82502bcf0ce0911ade41d6e2fab8ecae30b77d81d7bb5be2d43079033c964f395dd26e9fe8fc +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/clustalx/clustalx-2.1-r1.ebuild b/sci-biology/clustalx/clustalx-2.1-r1.ebuild new file mode 100644 index 000000000000..1d3ce97d942d --- /dev/null +++ b/sci-biology/clustalx/clustalx-2.1-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils qt4-r2 + +DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" +HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/" +SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND=" + dev-qt/qtcore:4 + dev-qt/qtgui:4" +RDEPEND="${DEPEND} + >=sci-biology/clustalw-${PV}" + +src_prepare() { + sed \ + -e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \ + -e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \ + -e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \ + -i ClustalQtParams.h || \ + die "Failed to patch shared files location." + sed \ + -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \ + -i HelpDisplayWidget.cpp || \ + die "Failed to patch help file location." + rm -rf usr || die +} + +src_install() { + dobin clustalx + insinto /usr/share/${PN} + doins colprot.xml coldna.xml colprint.xml clustalx.hlp + make_desktop_entry ${PN} ClustalX +} diff --git a/sci-biology/clustalx/clustalx-2.1-r2.ebuild b/sci-biology/clustalx/clustalx-2.1-r2.ebuild new file mode 100644 index 000000000000..6e9643755b69 --- /dev/null +++ b/sci-biology/clustalx/clustalx-2.1-r2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils qmake-utils + +DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" +HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/" +SRC_URI=" + http://www.clustal.org/download/current/${P}.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-qt/qtcore:4 + dev-qt/qtgui:4" +RDEPEND="${DEPEND} + >=sci-biology/clustalw-${PV}" + +src_prepare() { + sed \ + -e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \ + -e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \ + -e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \ + -i ClustalQtParams.h || \ + die "Failed to patch shared files location." + sed \ + -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \ + -i HelpDisplayWidget.cpp || \ + die "Failed to patch help file location." + rm -rf usr || die + default +} + +src_configure() { + eqmake4 +} + +src_install() { + dobin clustalx + insinto /usr/share/${PN} + doins colprot.xml coldna.xml colprint.xml clustalx.hlp + make_desktop_entry ${PN} ClustalX + doicon "${WORKDIR}"/${PN}.png +} diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/clustalx/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest new file mode 100644 index 000000000000..e997d2a6f419 --- /dev/null +++ b/sci-biology/consed/Manifest @@ -0,0 +1,10 @@ +AUX consed-29-fix-build-system.patch 5614 SHA256 652a970de74eebf12e7b7693bbbc953d4bb6662c29ab970d39c8b696ad0b2cfc SHA512 ea649079d5dbff21206bf8f56729fc559f374120dd3336499677eb65fde247739f41efdb29a3df60225ec38efc6802608aa2410bf4ab77f8d76bfd31fdc710fa WHIRLPOOL 597ee496f0a85371e9324d05c71350227945f6d436732347f4e86a2ccccdc59d948c41646bb78215275baa677d9e377dc88146267fd8d6cc01f4b32de4177482 +AUX consed-29-fix-c++14.patch 9261 SHA256 1cbd45895b083c3e8ff553f56da0e19d8e67866df8e38026e40252e20f8ab109 SHA512 be5cd76d36cf437c1113d09e540d98d0eb92b7e2e732f4a5a308066b8046b5628048203e791a0fa316e44a4cc127d027418a7f038406df22c3f60552f5b87789 WHIRLPOOL eddfeb0f11561107ff174adf0acfb3b6440f803b2b7410d372748fd1c2dad04185ca25e59c99a4d9c137af69f2f00be1bf9bf6a5813c5ca07a5afff6cee382f6 +AUX consed-29-fix-perl-shebang.patch 17375 SHA256 cdf3d2868fc69c2ff62897031d7e57e4b215b9d33ef07411fafd193fec2ea380 SHA512 4caed1ab7229e2b3e367f03a8d650cafed2974232fcd6daa08e62c90512d49e09caceb34c5bb65c67a588bab314165d72d8c1687393549d4107425df78e3218d WHIRLPOOL 7f7c36100a995f733bb126e637f470e4191cfd0dfb066ccce2fce6e7cd46cdc217811aed969c9235f5a9d64ecc032f6f3366a2744665c94ac486b714619cc6d7 +AUX consed-29-fix-qa.patch 11168 SHA256 8d024a5a8ac13411dfbe621ea7e9a968a802f2169822fb917085408e0d1eee44 SHA512 088d774159b421666bf75f6f9f17ee83d488625d482d8d404bde12671025b1f03322bee5c50e792fbbd822c223fa5ee697cf99c7efc9fcbebc119314d02df604 WHIRLPOOL d5464e848ad6af177963908eda8f18e7999faaaba50e67b05a9b7f365e24c6e6e49146afc922801b0f6ce7e6dbd372c2dc7c9709b3047aa3b2ded9f2e93cb9d6 +DIST consed-29-linux.tar.gz 36172715 SHA256 98354e2507ef9026b82c89db199ff1de7e4ec3686fccd691d215acdcde34ce39 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd WHIRLPOOL 26ebc1ee7114b0c609fd36c2c46b71c399bacb61f7db285ab36f296902964c14518c058e814a166b20a36c2d320280aeed0ca18b7104c6b503324bf27d4b57af +DIST consed-29-sources.tar.gz 3258845 SHA256 e7d3c2bf60e0bb22025e0416d16cf9864fec8091811ec285a39db4cb46bc3fc6 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 WHIRLPOOL 5ac363f049b6b40554112f830e812e7ab7d334a0f6707ea4da981ed1e468109f3bd7669382aa77e93cf12c78cc95fb1085711dcc972c7ff22ffe6b73056bb2c2 +EBUILD consed-29.ebuild 2701 SHA256 7470245178f4f819cc0f150a93bd69600be1419d1cc03568f4c8df812f03cffb SHA512 56d73a2d4ed207924c2a7676bfca84b8c0cc4f80d1a2a1b94fa2b3d644a6583f15e32ee81b9892122e051f17a1eda56d63ffb8d650283a9bee5c61bca6faf1d3 WHIRLPOOL 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91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild new file mode 100644 index 000000000000..d5417e310281 --- /dev/null +++ b/sci-biology/consed/consed-29.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="A genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI=" + ${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +COMMON_DEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + sci-biology/samtools:0.1-legacy +" +DEPEND=" + ${COMMON_DEPEND} + virtual/pkgconfig +" +RDEPEND=" + ${COMMON_DEPEND} + dev-lang/perl + >=sci-biology/phred-071220-r1 + >=sci-biology/phrap-1.080812-r2 +" + +S="${WORKDIR}" + +RESTRICT="fetch" +PATCHES=( + "${FILESDIR}/${PN}-29-fix-build-system.patch" + "${FILESDIR}/${PN}-29-fix-c++14.patch" + "${FILESDIR}/${PN}-29-fix-qa.patch" + "${FILESDIR}/${PN}-29-fix-perl-shebang.patch" +) + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + default + + sed \ + -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ + -e "s:/usr/local/genome:${EPREFIX}/usr:" \ + -e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \ + -e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \ + -i scripts/* contributions/* || die +} + +src_configure() { + append-cflags -std=gnu99 + append-lfs-flags +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \ + LIBS="-L${EPREFIX}/usr/$(get_libdir)" \ + X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \ + SAMTOOLS_LIBS="-lbam-0.1-legacy" +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/* + + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} + + if use examples; then + insinto /usr/share/${PN}/examples + doins -r \ + standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer + fi + + cat > 99consed <<-_EOF_ || die + CONSED_HOME=${EPREFIX}/usr + CONSED_PARAMETERS=${EPREFIX}/etc/consedrc + _EOF_ + doenvd 99consed + + dodoc README.txt *_announcement.txt +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch new file mode 100644 index 000000000000..27c9c552fe3f --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-build-system.patch @@ -0,0 +1,197 @@ +Make build system semi-sane: +* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS +* Remove default optimisation flags +* Remove -fpermissive from DEFS (as source builds fine now) +* Add large file support (LFS) via CPPFLAGS and not in Makefile + +--- a/makefile ++++ b/makefile +@@ -47,23 +47,20 @@ + # + # compilation + # +-CXX= g++ +-KRCC= gcc +-CC=gcc ++CXX ?= g++ ++CC ?= gcc + + # + # +-CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE ++DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE + +-OPT= -O + # + # Include directory for template classes must be included + # in both compilation & link lines, even if .h file is + # found in default path. C front, gotta love it. + # +-INC= -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18 ++INCLUDES = $(SAMTOOLS_CPPFLAGS) + +-DEPENDENCIES= + # + # + # Linking +@@ -80,12 +77,9 @@ + # /lib/ld-linux.so.2 (0x003ee000) + # + # To fix cut/paste bug, I've made X11 always dynamic. +-CLIBS= -lX11 +-LPATH= -L/usr/X11R6/lib +-ARCHIVES= /usr/X11R6/lib/libXm.a \ +-/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \ +-/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \ +-/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a ++ ++MOTIF_LIBS ?= -lXt -lXm ++ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS) + + + +@@ -94,7 +88,6 @@ + # + #LDFLGS= -g + # static linking +-LDFLGS= -g -rdynamic + + # + # the subdirectory used by cfront compilers gets cleaned +@@ -112,10 +105,10 @@ + # general compilation rules for .cpp, .cxx, .c files + # + .cpp.o: +- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< + + .c.o: +- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< + + # + # targets file included in generated makefile +@@ -593,17 +586,23 @@ + writeToRewriteReferenceFile.o \ + xsynchronize.o + ++SUBDIRS := misc/454 misc/mktrace misc/phd2fasta ++ ++all: consed $(SUBDIRS) ++ ++$(SUBDIRS): ++ $(MAKE) -C $@ ++ ++.PHONY: all $(SUBDIRS) ++ + consed: $(CONSED_OBJS) makefile checkLicenseKeyStub.o +- $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ +- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) + + trial_consed: $(CONSED_OBJS) makefile checkLicenseKey.o +- $(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \ +- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS) + + pure: $(CONSED_OBJS) makefile checkLicenseKeyStub.o +- $(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ +- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) + + clean: + rm -rf *.o core $(TEMPLATE_DIR) +@@ -613,15 +612,15 @@ + # the Solaris 5.x compiler cannot optimize the following + + consedResources.o: +- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp + + consedResources2.o: +- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp + + # tlingit cannot optimize the following: + + guiEditResources.o: +- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp + + guiEditResources.o : \ + assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \ +--- a/misc/454/Makefile ++++ b/misc/454/Makefile +@@ -0,0 +1,16 @@ ++CC ?= cc ++LIBM = -lm ++ ++DEFS = -DANSI_C ++ ++OBJS= sff2scf.c ++ ++sff2scf: $(OBJS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) ++ ++.c.o: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< ++ ++clean: ++ rm -f $(OBJS) sff2scf ++ +--- a/misc/mktrace/Makefile ++++ b/misc/mktrace/Makefile +@@ -1,13 +1,17 @@ +-CC= cc +-CFLAGS= -g +-CLIB= -lm ++CC ?= cc ++LIBM = -lm ++ ++DEFS = -DANSI_C + + OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \ + freeTrace.o rwUtil.o writePhd.o getTime.o \ + readQUAL.o + + mktrace: $(OBJS) +- $(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) ++ ++.c.o: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< + + clean: + rm -f $(OBJS) mktrace +--- a/misc/phd2fasta/Makefile ++++ b/misc/phd2fasta/Makefile +@@ -1,8 +1,9 @@ +-CC=cc +-CFLAGS=-O -w +-CLIB=-lm ++CC ?= cc ++LIBM = -lm + +-OBJ= phd2fasta.o \ ++DEFS = -DANSI_C ++ ++OBJS= phd2fasta.o \ + readParam.o initParam.o checkParam.o \ + freeParam.o helpParam.o \ + readFOF.o readDIR.o readFOX.o \ +@@ -15,10 +16,11 @@ + + INC= phd2fasta.h + +-SRC = $(OBJ:.o=.c) +- +-phd2fasta: $(OBJ) +- $(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB) ++phd2fasta: $(OBJS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) ++ ++.c.o: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< + + clean: + rm -f $(OBJ) phd2fasta diff --git a/sci-biology/consed/files/consed-29-fix-c++14.patch b/sci-biology/consed/files/consed-29-fix-c++14.patch new file mode 100644 index 000000000000..212b8d63d1e3 --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-c++14.patch @@ -0,0 +1,376 @@ +Fix building with C++14: +* Add 'noexcept(false)' to throwing destructors in C++11 mode +* Properly guard C declarations with extern "C" scopes +* Avoid erroneous overloaded suffix operator errors, due to missing spaces +* Add explicit casts to avoid -Wnarrowing errors +* Add 'this->' for dependent identifiers in derived class templates, + previously required -fpermissive + +--- a/bvAlignedReads.cpp ++++ b/bvAlignedReads.cpp +@@ -126,7 +126,11 @@ + } + + +-bvAlignedReads :: ~bvAlignedReads() { ++bvAlignedReads :: ~bvAlignedReads() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++{ + + + assert( pBamView_->aBVAlignedReads_.remove( this ) ); +--- a/bvAlignedReads.h ++++ b/bvAlignedReads.h +@@ -81,7 +81,11 @@ + const FileName& filReferenceSequenceFile, + bamView* pBamView ); + +- ~bvAlignedReads(); ++ ~bvAlignedReads() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + bool operator==( const bvAlignedReads& myBVAlignedReads ) const { + return( this == &myBVAlignedReads ); +--- a/chromatData.h ++++ b/chromatData.h +@@ -58,6 +58,9 @@ + #ifndef CHROMATDATA_DEFINED + #define CHROMATDATA_DEFINED + ++#ifdef __cplusplus ++extern "C" { ++#endif + + #ifndef FLOAT + #define FLOAT double +@@ -131,4 +134,8 @@ + int freeChromatData(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/compareContigs.cpp ++++ b/compareContigs.cpp +@@ -126,6 +126,9 @@ + + + compareContigs :: ~compareContigs() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + + if ( !bCalledFromMakeJoins_ ) { +--- a/compareContigs.h ++++ b/compareContigs.h +@@ -137,7 +137,11 @@ + compareContigs( ContigWin* pContigWin, const int nConsPos1); + compareContigs(); // for assemblyView + +- ~compareContigs(); ++ ~compareContigs() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + // this makes RWTPtrOrderedVector in ConsEd happy + bool operator==( const compareContigs& compC ) const { + +--- a/filePopupAndGetAceFilename.cpp ++++ b/filePopupAndGetAceFilename.cpp +@@ -317,7 +317,7 @@ + struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); + + strftime( szDateTime, nDateTimeSize, +- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", ++ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", + pTM ); + + RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); +@@ -620,7 +620,7 @@ + struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); + + strftime( szDateTime, nDateTimeSize, +- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", ++ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", + pTM ); + + RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); +--- a/findTraceExtrema.h ++++ b/findTraceExtrema.h +@@ -44,8 +44,15 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + int findTraceExtrema( ChromatData *chromatData ); + ++#ifdef __cplusplus ++} ++#endif + + #endif + +--- a/makeUpper.h ++++ b/makeUpper.h +@@ -42,6 +42,14 @@ + #ifndef MAKEUPPER_INCLUDED + #define MAKEUPPER_INCLUDED + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + void makeUpper( char* szStringOfMixedCase ); + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/nextPhredPipeline.cpp ++++ b/nextPhredPipeline.cpp +@@ -476,7 +476,7 @@ + void nextPhredPipeline :: openAndLockControlFile() { + + +- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR ); ++ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600); + if ( nFDControlFile_ == -1 ) { + THROW_FILE_ERROR( filControlFile_ ); + } +--- a/readABI.h ++++ b/readABI.h +@@ -56,10 +56,18 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + #ifdef ANSI_C + ChromatData *readABI( char *fn, int *status ); + #else + ChromatData *readABI(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/readData.h ++++ b/readData.h +@@ -44,6 +44,14 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + ChromatData *readData( char *filename, int* status ); + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/readESD.h ++++ b/readESD.h +@@ -53,6 +53,10 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + typedef unsigned int4 DWORD; + typedef unsigned char TCHAR; + typedef char BYTE; +@@ -187,5 +191,7 @@ + ChromatData *readESD(); + #endif + +- ++#ifdef __cplusplus ++} ++#endif + +--- a/readSCF.h ++++ b/readSCF.h +@@ -56,6 +56,10 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + /* ---- Constants ---- */ + #define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f') + #define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX ) +@@ -144,4 +148,8 @@ + int readSCF3(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif +--- a/readsense_bitmaps.h ++++ b/readsense_bitmaps.h +@@ -56,10 +56,10 @@ + static const int forward_bitmap_height = 19; + static char forward_bitmap_bits[] = { + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, +- 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, +- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0xff, 0x3f, 0x00, 0xf8, 0xff, 0xff, 0x07, +- 0xf8, 0xff, 0xff, 0x0f, 0xf8, 0xff, 0xff, 0x07, 0xf8, 0xff, 0x1f, 0x00, +- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, ++ 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, ++ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, (char)0xff, 0x3f, 0x00, (char)0xf8, (char)0xff, (char)0xff, 0x07, ++ (char)0xf8, (char)0xff, (char)0xff, 0x0f, (char)0xf8, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, 0x1f, 0x00, ++ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, + 0x00, 0x00, 0x00, 0x00}; + +@@ -67,10 +67,10 @@ + static const int reverse_bitmap_height = 19; + static char reverse_bitmap_bits[] = { + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, +- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, 0xf8, 0x07, +- 0x00, 0xc0, 0xff, 0x07, 0x00, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, +- 0xfc, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, 0x00, 0xfe, 0xff, 0x07, +- 0x00, 0xc0, 0xff, 0x07, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, ++ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, (char)0xf8, 0x07, ++ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, ++ (char)0xfc, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, 0x00, (char)0xfe, (char)0xff, 0x07, ++ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, + 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, + 0x00, 0x00, 0x00, 0x00}; + +--- a/readType.h ++++ b/readType.h +@@ -56,11 +56,19 @@ + + #include "chromatData.h" + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + #ifdef ANSI_C + int readType( char *filename ); + #else + int readType(); + #endif + ++#ifdef __cplusplus ++} ++#endif ++ + #endif + +--- a/rwtptrsortedvector.h ++++ b/rwtptrsortedvector.h +@@ -57,7 +57,6 @@ + #ifdef USE_USING_IN_PUBLIC_TEMPLATE_CLASSES + using RWTPtrOrderedVector<TP>::nCurrentLength_; + using RWTPtrOrderedVector<TP>::isEmpty; +- using RWTPtrOrderedVector<TP>::nCurrentLength_; + using RWTPtrOrderedVector<TP>::length; + using RWTPtrOrderedVector<TP>::ppArray_; + using RWTPtrOrderedVector<TP>::data; +@@ -84,7 +83,7 @@ + if ( nInsertBeforeIndex == RW_NPOS ) + nInsertBeforeIndex = nCurrentLength_; + +- insertAt( nInsertBeforeIndex, pVal ); ++ this->insertAt( nInsertBeforeIndex, pVal ); + } + + // don't copy this. copy mbtValOrderedVectorOfRWCString's method instead +--- a/rwtvalsortedvector.h ++++ b/rwtvalsortedvector.h +@@ -74,7 +74,7 @@ + if ( nPos == RW_NPOS ) + nPos = nCurrentLength_; + +- insertAt( nPos, val ); ++ this->insertAt( nPos, val ); + } + + +--- a/rwUtil.h ++++ b/rwUtil.h +@@ -51,6 +51,10 @@ + *|***************************************************************************|* + */ + ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + #ifdef ANSI_C + int2 inSwpSint2( char *ptr ); + int4 inSwpSint4( char *ptr ); +@@ -97,3 +101,6 @@ + int writeUint4(); + #endif + ++#ifdef __cplusplus ++} ++#endif +--- a/soGetDateTime.cpp ++++ b/soGetDateTime.cpp +@@ -62,13 +62,13 @@ + else if ( nFormat == nDotInMiddle ) { + strftime( szDateTime, + nDateTimeSize, +- "%y%m%d."quote(%H)quote(%M)quote(%S), ++ "%y%m%d." quote(%H)quote(%M)quote(%S), + localtime( &timee ) ); + } + else { + strftime( szDateTime, + nDateTimeSize, +- "%y%m%d:"quote(%H)quote(%M)quote(%S), ++ "%y%m%d:" quote(%H)quote(%M)quote(%S), + localtime( &timee ) ); + } + +--- a/szGetTime.h ++++ b/szGetTime.h +@@ -42,9 +42,15 @@ + #ifndef szGetTime_included + #define szGetTime_included + +-char *szGetTime(); ++#ifdef __cplusplus ++extern "C" { ++#endif + ++char *szGetTime(); + ++#ifdef __cplusplus ++} ++#endif + + #endif + diff --git a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch new file mode 100644 index 000000000000..a27a3537a8d1 --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch @@ -0,0 +1,701 @@ +Make perl shebangs portable, such that the scripts can also be used on Gentoo Prefix. +Rationale: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/contributions/ace2fof ++++ b/contributions/ace2fof +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # .-----------------------------------------------------------------------------------. + # | | +@@ -107,6 +107,7 @@ + # | | + # `-----------------------------------------------------------------------------------' + #Fixed this file for taking Aracne's Ace file by syang 05152002 ++use warnings; + use strict; + use POSIX qw(fmod); + +--- a/contributions/ace2OligosWithComments.perl ++++ b/contributions/ace2OligosWithComments.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # ace2Oligos.perl + # +@@ -18,6 +18,8 @@ + # Rev: 020528 to print comments in oligo tags upon request (Peter Kos) + # + ++use warnings; ++ + $szUsage = "\nUsage: $0 (name of ace file) (name of oligo file) [Print|Comment|PrintComment]\n"; + + die "$szUsage" if (( $#ARGV != 1 ) && ( $#ARGV != 2 )); +--- a/contributions/aceContigs2Phds.perl ++++ b/contributions/aceContigs2Phds.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # aceContigs2Phd.perl + # +@@ -13,6 +13,8 @@ + # Acknowledgements: Borrowed as much as I could from determineReadTypes.Perl + # and fasta2Phd.perl + ++use warnings; ++ + $szUsage = "Usage: aceContigs2Phds.perl [-s minimum-contig-size] <name of ace file>"; + $nContigLimit = 2000; + +--- a/contributions/acestatus.pl ++++ b/contributions/acestatus.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # acestatus.pl + # author: Cliff Wollam +@@ -14,6 +14,7 @@ + # USAGE FROM THE COMMAND LINE: + # acestatus.pl ace_filename + ++use warnings; + use strict; + + if($#ARGV >= 0) { +--- a/contributions/cons.perl ++++ b/contributions/cons.perl +@@ -1,5 +1,6 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + ++use warnings; + use strict; + use Cwd; + +--- a/contributions/mergeAces.perl ++++ b/contributions/mergeAces.perl +@@ -1,4 +1,4 @@ +-#! /usr/local/bin/perl -w ++#!/usr/bin/env perl + + # Bugs and complaints to Bill Gilliland, billg@ucdavis.edu. + # mergeAces.perl v. 0.2 5/22/01 +@@ -9,6 +9,7 @@ + # project directory (if it doesn't already exist) with all the cgrams + # and phd files of the original projects. + ++use warnings; + use Getopt::Long; + use File::Copy; + $pathRoot = $ENV{"PWD"}; +--- a/contributions/phredPhrapWithPhdBalls ++++ b/contributions/phredPhrapWithPhdBalls +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # phredPhrapWithPhdBalls + # modified from phredPhrap by Ben Allen at LANL +@@ -73,6 +73,7 @@ + # Rev: 120312 to not duplicate consensus tags during miniassembly + # Rev: 120717 Ben Allen (LANL) to use reads from phdballs as well as phd_dir + ++use warnings; + + $szVersion = "120312"; + +--- a/contributions/recover_consensus_tags ++++ b/contributions/recover_consensus_tags +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # Purpose: Transfers all consensus tags from a set of old assemblies to + # a new assembly. +@@ -14,6 +14,7 @@ + # rct ace_filename <only ace file to be transfer (optional)> + # You must be in the edit_dir where the ace file is located + ++use warnings; + use strict; + + +--- a/contributions/revert_fof ++++ b/contributions/revert_fof +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: If the user really screws up a read, to back out all changes. + # You must reassemble after using this. +@@ -19,6 +19,8 @@ + # phd extensions. + # revert_fof use file of files to give reads to revert 3/14/01 SL + ++use warnings; ++ + $szUsage = "Enter a file of files name, please!"; + + die $szUsage if ( $#ARGV != 0 ); +--- a/contributions/sff2phd.perl ++++ b/contributions/sff2phd.perl +@@ -1,4 +1,5 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++use warnings; + use strict; + # SFF to PHD files converter, with 454 paired reads and MID support + # Version 0.15 - 111229 +--- a/contributions/sff2phd_Samborskyy ++++ b/contributions/sff2phd_Samborskyy +@@ -1,4 +1,5 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++use warnings; + use strict; + # SFF to PHD files converter, with 454 paired reads and MID support + # Version 0.10 - 101110 +--- a/scripts/ace2Fasta.perl ++++ b/scripts/ace2Fasta.perl +@@ -1,7 +1,9 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Purpose: makes a contigs file out of an ace file + ++use warnings; ++ + $szUsage = "Usage: ace2Contigs.perl (ace file)"; + + +--- a/scripts/ace2Oligos.perl ++++ b/scripts/ace2Oligos.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # ace2Oligos.perl + # +@@ -16,6 +16,8 @@ + # Rev: 000330 to handle comments in oligo tags + # + ++use warnings; ++ + $szUsage = "Usage: ace2Oligos.perl (name of ace file) (name of oligo file)"; + + if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { +--- a/scripts/add454Reads.perl ++++ b/scripts/add454Reads.perl +@@ -1,11 +1,11 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # add454Reads.perl + # part of Consed package + # + # DG with help from Hao Wang to screen vector + +- ++use warnings; + use File::Basename; + + +--- a/scripts/addReads2Consed.perl ++++ b/scripts/addReads2Consed.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Purpose: called by consed in order to add new reads to an + # existing assembly without reassemblying +@@ -29,6 +29,7 @@ + # Rev: 080320 (David Gordon) to use discrep_lists instead of alignments + # Rev: 130828 (David Gordon) to handle slashes (/) in read names + ++use warnings; + + $szVersion = "130828"; + if ( $#ARGV >= 0 ) { +--- a/scripts/addSangerReads.perl ++++ b/scripts/addSangerReads.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # addSangerReads.perl + +@@ -32,7 +32,7 @@ + # added is printed in a report ending with ".log". The name of this + # file is listed in auto.fof + +- ++use warnings; + + + $szVersion = "120717"; +--- a/scripts/addSolexaReads.perl ++++ b/scripts/addSolexaReads.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # addSolexaReads.perl + +@@ -54,7 +54,7 @@ + + $szUsage = "addSolexaReads.perl -ace (ace file) -fastqfof (solexa files) -fasta (fasta file) -readsList (file of list of desired reads) where -readsList is optional"; + +- ++use warnings; + use Getopt::Long; + + GetOptions( "ace=s" => \$szAceFile, +--- a/scripts/alignRNA2Genomic.perl ++++ b/scripts/alignRNA2Genomic.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # alignRNA2Genomic.perl + +@@ -6,6 +6,8 @@ + # consed-ready ace and phd ball with the RNA aligned against the + # genomic with introns being represented by large gaps + ++use warnings; ++ + $szVersion = "120717"; + + if ( $#ARGV == 0 ) { +--- a/scripts/alignSolexaReads2Refs.perl ++++ b/scripts/alignSolexaReads2Refs.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # Input: a file where each line looks like this: + # (solexa seq file) (read prefix) +@@ -10,6 +10,7 @@ + + # Output: a list of alignment files + ++use warnings; + + defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || + ( $szConsedHome = "/usr/local/genome" ); +--- a/scripts/amplifyTranscripts.perl ++++ b/scripts/amplifyTranscripts.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: runs consed -autoPCRAmplify in order to pick pcr primers + # for a large group of regions +@@ -40,7 +40,7 @@ + # That is, the left primers are given in top strand orientation, and + # the right primers are given in bottom strand orientation. + +- ++use warnings; + + defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || + ( $szConsedHome = "/usr/local/genome" ); +--- a/scripts/autoPrimers.perl ++++ b/scripts/autoPrimers.perl +@@ -1,5 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + ++use warnings; + + $szUsage = "autoPrimers.perl (fasta file of targets)"; + $szVersion = "141226"; +--- a/scripts/bam2Ace.perl ++++ b/scripts/bam2Ace.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + + # Purpose: runs: +@@ -6,6 +6,7 @@ + # 2) consed -renameDuplicates + # 3) consed -removeColumnsOfPads + ++use warnings; + + $szUsage = "usage: bam2Ace.perl -bamFile (bam file) -regionsFile (regions file) (see README.txt for format of the regions file) -exec (consed executable name) -newAceFile (new ace file name) where the -exec (exec) is optional"; + +--- a/scripts/convertBedToBamScape.perl ++++ b/scripts/convertBedToBamScape.perl +@@ -1,4 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + + $szUsage = "usage: convertBedToBamScape.perl (Bed file) (BamScape file) (fasta file of all sequences) (conversion of reference names--optional)"; + +--- a/scripts/countEditedBases.perl ++++ b/scripts/countEditedBases.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # countEditedBases.perl + # +@@ -11,6 +11,8 @@ + # + # + ++use warnings; ++ + while(<>) { + if ( /^CO / ) { + @aWords = split; +--- a/scripts/determineReadTypes.perl ++++ b/scripts/determineReadTypes.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # determineReadTypes.perl + # + # Purpose: to write into the phd file information about the template +@@ -173,6 +173,7 @@ + # + ############################################################### + ++use warnings; + + # you can remove or comment out this line when you are satisfied with + # your customized version of this file. +--- a/scripts/fasta2Ace.perl ++++ b/scripts/fasta2Ace.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # manyFasta2Ace.perl + # +@@ -13,6 +13,7 @@ + # + # NOTE: you must run this in edit_dir + ++use warnings; + use Getopt::Long; + + $szRevision = "141212"; +--- a/scripts/fasta2PhdBall.perl ++++ b/scripts/fasta2PhdBall.perl +@@ -1,4 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + + $nQuality = 20; + +--- a/scripts/fasta2Phd.perl ++++ b/scripts/fasta2Phd.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # fasta2Phd.perl + # +@@ -20,6 +20,7 @@ + # June 2002, Bill Gilliland to allow the user to specify + # the quality value + ++use warnings; + use Getopt::Long; + GetOptions( "quality=i" => \$qualityValue); + +--- a/scripts/fastq2Phrap.perl ++++ b/scripts/fastq2Phrap.perl +@@ -1,4 +1,6 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + + $szUsage = "fastq2Phrap.perl (fastq) or for paired reads fastq2Phrap.perl (fastq1) (fastq2) where fastq1 and fastq2 have corresponding mate pairs--e.g., the 5th read in fastq1 is the mate of the 5th read in fastq2--these fastq files are assumed to be in ../solexa_dir--not the current directory\n"; + +--- a/scripts/filter454Reads.perl ++++ b/scripts/filter454Reads.perl +@@ -1,6 +1,6 @@ +-#!/usr/bin/perl -w +- ++#!/usr/bin/env perl + ++use warnings; + use File::Basename; + + +--- a/scripts/findSequenceMatchesForConsed.perl ++++ b/scripts/findSequenceMatchesForConsed.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # findSequenceMatchesForConsed.perl + +@@ -16,6 +16,8 @@ + # REVISIONS: 021127 (DG) to write (project).(date).(time).fasta instead of + # (project).fasta.screen.ace.1.(date).(time).fasta + ++use warnings; ++ + $szVersion = "021127"; + + $szUsage = "Usage: findSequenceMatchesForConsed.perl (ace file) (crossmatch parameters, if any)"; +--- a/scripts/fixContigEnd.perl ++++ b/scripts/fixContigEnd.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # fixContigEnd.perl + +@@ -7,6 +7,7 @@ + # consed -ace (acefile) -fixContigEnds + # + ++use warnings; + + $szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)"; + +--- a/scripts/lib2Phd.perl ++++ b/scripts/lib2Phd.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # lib2Phd.perl + # +@@ -23,6 +23,8 @@ + # accept fasta library files as input. The output file is named + # according to the first, non-space block of text on each fasta defline. + ++use warnings; ++ + $nQuality = 20; + + $szUsage = "Usage: lib2Phd.perl <name of file with fasta library>"; +--- a/scripts/makePhdBall.perl ++++ b/scripts/makePhdBall.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: concatenate all phd file into a single phd.ball + # for the purpose of fast startup of consed +@@ -9,6 +9,7 @@ + # + # February 2008, David Gordon + ++use warnings; + + if ( $#ARGV >= 0 ) { + if ( $ARGV[0] eq "-v" || $ARGV[0] eq "-V" ) { +--- a/scripts/makeRegionsFile.perl ++++ b/scripts/makeRegionsFile.perl +@@ -1,10 +1,12 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # makeRegionsFile.perl + # To be used with consed -bam2Ace + # Takes a fasta file of sequences and makes a regions file that + # specifies the entire length of each sequence. + ++use warnings; ++ + $szUsage = "makeRegionsFile.perl (name of fasta file)"; + + $szVersion = "110914"; +--- a/scripts/orderPrimerPairs.perl ++++ b/scripts/orderPrimerPairs.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: puts the primers in 96 well format for ordering. + # creates a file that can be emailed to +@@ -13,6 +13,8 @@ + # 2) a file of primer pairs, sorted by product size + # 3) a fasta file of the primers, for your convenience for analysis + ++use warnings; ++ + $| = 1; + + $szUsage = "orderPrimerPairs.perl"; +--- a/scripts/phd2Ace.perl ++++ b/scripts/phd2Ace.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # phd2Ace.perl + # +@@ -13,6 +13,8 @@ + # REV: 981002 (David Gordon) for new ace format + # 981210 (DG) to eliminate warning message + ++use warnings; ++ + $szPhdDirPath = "../phd_dir"; + + $szUsage = "Usage: phd2Ace.perl <filename (without directory) of phd file>\nThe phd file is assumed to reside in $szPhdDirPath"; +--- a/scripts/phredPhrap ++++ b/scripts/phredPhrap +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # phredPhrap + # +@@ -70,6 +70,8 @@ + # Rev: 110609 to allow masking of vector sequence when doing miniassemblies + # Rev: 120312 to not duplicate consensus tags during miniassembly + ++use warnings; ++ + $szVersion = "120312"; + + +--- a/scripts/picard2Regions.perl ++++ b/scripts/picard2Regions.perl +@@ -1,10 +1,12 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # PURPOSE: takes a file of locations in the format for bamScape custom + # navigation (Picard IntervalList format), adds 2000 bases of context + # to each side of each location, and prints a region file in format to + # be used by bam2Ace + ++use warnings; ++ + $szRevision = "140903"; # David Gordon + + if ( defined( $ARGV[0] ) && +--- a/scripts/removeReads ++++ b/scripts/removeReads +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # PURPOSE: removes a list of chromats from an assembly. After running this, + # you must reassemble to create an ace file without the given phd files. +@@ -16,6 +16,8 @@ + # removeReads (name of fof's) + # + ++use warnings; ++ + $szUsage = "Usage: removeReads listOfReads.fof"; + + die "$szUsage" if ( $#ARGV != 0 ); +--- a/scripts/revertToUneditedRead ++++ b/scripts/revertToUneditedRead +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # PURPOSE: If the user really screws up a read, to back out all changes. + # You must reassemble after using this. +@@ -16,6 +16,7 @@ + # REV: 7/24/98 (DG) + # REV: 8/28/2013 (DG) to handle readnames with slashes (/) + ++use warnings; + + $szUsage = "Usage: revertToUneditedRead (read name without any .phd.# extension)"; + +--- a/scripts/selectOneRegion.perl ++++ b/scripts/selectOneRegion.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # selectOneRegion.perl + # +@@ -11,6 +11,7 @@ + # and you will create an ace file chr15_51000000.ace or chr15_51000000.ace.1 + # (or higher extension) + ++use warnings; + use Getopt::Long; + + +--- a/scripts/selectRegions.perl ++++ b/scripts/selectRegions.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + # selectRegions.perl + # +@@ -43,7 +43,7 @@ + # my_new_ace.ace says what the ace file should be called (the + # extension may not start at 1 if there is already a .1 + +- ++use warnings; + + $SIG{__WARN__} = dieWhenGetWarning; + sub dieWhenGetWarning { +--- a/scripts/tagRepeats.perl ++++ b/scripts/tagRepeats.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # PROGRAM: tagRepeats.perl + # PURPOSE: to put consensus tags on any found ALU or any other +@@ -10,6 +10,7 @@ + # INPUTS: The ace file. You must also provide a fasta file of the + # ALU or any other sequence you want to tag + ++use warnings; + + $szVersion = "090209"; + if ( $#ARGV >= 0 ) { +--- a/scripts/testSocket.perl ++++ b/scripts/testSocket.perl +@@ -1,7 +1,8 @@ +-#! /usr/local/bin/perl -w ++#!/usr/bin/env perl + + # open a socket to consed +- ++ ++use warnings; + use IO::Socket; + + # Consed makes a file which has nothing but the port number. +--- a/scripts/transferConsensusTags.perl ++++ b/scripts/transferConsensusTags.perl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Purpose: Transfers consensus tags from an old assembly to + # a new assembly. +@@ -44,6 +44,8 @@ + # Nov 2001, DG to handle cloneEnd tags which have orientation + # Mar 2012, DG to prevent duplicating tags after miniassembly + ++use warnings; ++ + $szUsage = "Usage: transferConsensusTags.perl (old ace file) (new ace file) (file of list of old contigs with consensus tags to be transferred)"; + + if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch new file mode 100644 index 000000000000..5bdf0264d25b --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-qa.patch @@ -0,0 +1,275 @@ +Fix various QA violations, due to +* implicit declarations +* incorrect printf() format specifiers +* incorrect function prototypes +* remove unsafe gets() fucntion + +--- a/misc/454/sff2scf.c ++++ b/misc/454/sff2scf.c +@@ -39,6 +39,7 @@ + void writeScfFile(char *filearg, char *outfile); + void writeScfCommand(char *filearg, char *outfile); + ++int sffinfo(int argc, char *argv[], FILE* pTempFile ); + + int main(int argc, char *argv[]) + { +--- a/misc/mktrace/mktrace.c ++++ b/misc/mktrace/mktrace.c +@@ -70,9 +70,9 @@ + else + { + printf( "enter FASTA filename: " ); +- gets( ifnm ); ++ fgets( ifnm, sizeof(ifnm), stdin ); + printf( "enter output filename: " ); +- gets( ofnm ); ++ fgets( ofnm, sizeof(ofnm), stdin ); + } + + /* +@@ -192,7 +192,7 @@ + /* + ** Write phd file. + */ +- if( writePhd( ofnm, numBase, seq, qual, pos, numPoint, trace ) == ERROR ) ++ if( writePhd( ofnm, numBase, seq, qual, pos, numPoint ) == ERROR ) + { + fprintf( stderr, "mktrace: error: bad status: writePhd\n" ); + free( seq ); +--- a/misc/mktrace/mktrace.h ++++ b/misc/mktrace/mktrace.h +@@ -37,8 +37,8 @@ + int writeSCF( char *filename, int numBase, char *seq, int numPoint, float **trace ); + int freeTrace( float **trace ); + char *readFASTA( char *filename, char *entryName, char *comments, int *len ); +-int writePhd( char *ofnm, int numBase, char *seq, int *pos, int numPoint ); + int *readQUAL( char *filename, char *entryName, char *comments, int *len ); ++char *getTime( void ); + #else + int writePhd(); + float **synTrace(); +--- a/misc/phd2fasta/phd2fasta.h ++++ b/misc/phd2fasta/phd2fasta.h +@@ -276,6 +276,10 @@ + Comments *comments, Seq *seq, TagList *tagList, char *emsg ); + int checkIntString( char *string ); + int delimiterTest( char *string, unsigned int mask ); ++int checkParam( Option *option ); ++char* getVersion( void ); ++int showDoc( void ); ++char* getTime( void ); + #else + Option *getOption(); + struct Tag *allocTag(); +--- a/misc/phd2fasta/readStdTag.c ++++ b/misc/phd2fasta/readStdTag.c +@@ -699,11 +699,11 @@ + if( fstat ) + { + fprintf( stderr, +- "readStdTag: %s: line: %d: unexpected delimiter %s\n", ++ "readStdTag: %s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", ++ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +--- a/misc/phd2fasta/readWholeReadTag.c ++++ b/misc/phd2fasta/readWholeReadTag.c +@@ -393,11 +393,11 @@ + if( fstat ) + { + fprintf( stderr, +- "readWholeReadTag: %s: line: %d: unexpected delimiter %s\n", ++ "readWholeReadTag: %s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", ++ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", + filename, + nline, + line ); +--- a/misc/phd2fasta/writeFasta.c ++++ b/misc/phd2fasta/writeFasta.c +@@ -39,7 +39,7 @@ + #include "phd2fasta.h" + + #ifdef ANSI_C +-writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, ++int writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, + int outBasePosOption, + Comments *comments, Seq *seq, TagList *tagList, char *emsg ) + #else +--- a/motifutils.cpp ++++ b/motifutils.cpp +@@ -202,13 +202,13 @@ + void printButtonEvent( XButtonEvent* pEvent ) { + + printf( "type = %d\n", pEvent->type ); +- printf( "serial = %d\n", pEvent->serial ); ++ printf( "serial = %lu\n", pEvent->serial ); + printf( "send_event = %s\n", szPrintBool( pEvent->send_event ) ); +- printf( "*display = %x\n", pEvent->display ); +- printf( "window = %x\n", pEvent->window ); +- printf( "root = %x\n", pEvent->root ); +- printf( "subwindow = %x\n", pEvent->subwindow ); +- printf( "time = %d\n", pEvent->time ); ++ printf( "*display = %p\n", pEvent->display ); ++ printf( "window = %lu\n", pEvent->window ); ++ printf( "root = %lu\n", pEvent->root ); ++ printf( "subwindow = %lu\n", pEvent->subwindow ); ++ printf( "time = %lu\n", pEvent->time ); + printf( "x = %d\n", pEvent->x ); + printf( "y = %d\n", pEvent->y ); + printf( "x_root = %d\n", pEvent->x_root ); +--- a/phaster2PhdBall.cpp ++++ b/phaster2PhdBall.cpp +@@ -547,7 +547,7 @@ + + int nTokens = + sscanf( soLine_.data(), +- "%s %*s %d %d %lld %s %s %*s %d %d %lld %s %s\n", ++ "%s %*s %d %d %ld %s %s %*s %d %d %ld %s %s\n", + soReadName_.data(), + &nRead1Left_, + &nRead1Right_, +--- a/printAutoFinishMiscInfo.cpp ++++ b/printAutoFinishMiscInfo.cpp +@@ -80,7 +80,7 @@ + int nError = stat( (char*) soAceFileFullPathname.data(), &statBuffer ); + + if (nError == 0 ) { +- fprintf( pAO,"size: %d date: %s\n", ++ fprintf( pAO,"size: %ld date: %s\n", + (long) statBuffer.st_size, + ctime( &( statBuffer.st_mtime )) ); + +--- a/printAutoFinishParameters.cpp ++++ b/printAutoFinishParameters.cpp +@@ -206,7 +206,7 @@ + pCP->nInexactSearchForStringMaxPerCentMismatch_ ); + + fprintf( pAO, "! when using the inexact search for string, allow up to this\n"); +- fprintf( pAO, "! % mismatch: the sum of the insertion, deletion, and substitution\n"); ++ fprintf( pAO, "! %% mismatch: the sum of the insertion, deletion, and substitution\n"); + fprintf( pAO, "! differences divided by the length of the query string\n"); + fprintf( pAO, "! (YES)\n"); + fprintf( pAO, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n", +@@ -825,7 +825,7 @@ + fprintf( pAO, "! template will be 1500 bases from the forward read. But if this template\n"); + fprintf( pAO, "! has an insert that is shorter than average, the walk may walk into vector.\n"); + fprintf( pAO, "! To be conservative, we may want to assume that the insert is somewhat \n"); +- fprintf( pAO, "! shorter than average. By default, we assume that it is 90% as large as \n"); ++ fprintf( pAO, "! shorter than average. By default, we assume that it is 90%% as large as \n"); + fprintf( pAO, "! the average. This parameter gives that percentage. This parameter\n"); + fprintf( pAO, "! is used both by Consed and Autofinish.\n"); + fprintf( pAO, "! (OK)\n"); +@@ -1249,9 +1249,9 @@ + pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); + + fprintf( pAO, "! Autofinish computes the per cent of existing reads are aligned at\n"); +- fprintf( pAO, "! each base position. Typically, this number starts at around 0% at\n"); +- fprintf( pAO, "! base position 1, rises to close to 100% at around base position 300,\n"); +- fprintf( pAO, "! and then drops again to 0% at base position 800 or so. This number\n"); ++ fprintf( pAO, "! each base position. Typically, this number starts at around 0%% at\n"); ++ fprintf( pAO, "! base position 1, rises to close to 100%% at around base position 300,\n"); ++ fprintf( pAO, "! and then drops again to 0%% at base position 800 or so. This number\n"); + fprintf( pAO, "! specifies how high the number must be for Autofinish to consider an\n"); + fprintf( pAO, "! Autofinish read to cover a single subclone region.\n"); + fprintf( pAO, "! (OK)\n"); +@@ -1295,7 +1295,7 @@ + ( ( pCP->bCheckIfTooManyWalks_ ) ? "true" : "false" ) ); + + fprintf( pAO, "! this just checks if the number of walks, pcr ends, and unknown reads\n"); +- fprintf( pAO, "! exceeds 20% of the total number of reads. If this is exceeded, then \n"); ++ fprintf( pAO, "! exceeds 20%% of the total number of reads. If this is exceeded, then \n"); + fprintf( pAO, "! a warning message is given. Typically, such a warning indicates\n"); + fprintf( pAO, "! that you have incorrectly customized determineReadTypes.perl\n"); + fprintf( pAO, "! (OK)\n"); +@@ -1446,7 +1446,7 @@ + ( ( pCP->bProcessMatePairsAtStartup_ ) ? "true" : "false" ) ); + + fprintf( pAO, "! This is necessary to show the mate pair flags, but it does add\n"); +- fprintf( pAO, "! around 15% to startup time.\n"); ++ fprintf( pAO, "! around 15%% to startup time.\n"); + fprintf( pAO, "! (OK)\n"); + fprintf( pAO, "consed.maximumNumberOfTracesShown: %d\n", + pCP->nMaximumNumberOfTracesShown_ ); +@@ -1796,7 +1796,7 @@ + (char*)pCP->soStoreTracePeakPositions_.data() ); + + fprintf( pAO, "! never, always or whenChromatAvailable\n"); +- fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%,\n"); ++ fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%%,\n"); + fprintf( pAO, "! especially if the assembler is Newbler. always means it will store\n"); + fprintf( pAO, "! the positions if they are present in the phd file/ball.\n"); + fprintf( pAO, "! \"whenChromatAvailable\" means it will store trace peak positions for\n"); +--- a/readPrimerScreenSequences.cpp ++++ b/readPrimerScreenSequences.cpp +@@ -167,7 +167,7 @@ + ++nSequenceNumber ) { + if ( pnLengthOfSequence[ nSequenceNumber ] != + strlen( pszSequence[ nSequenceNumber ] ) ) { +- sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %d for sequence number %d", ++ sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %zu for sequence number %d", + pnLengthOfSequence[ nSequenceNumber ], + strlen( pszSequence[ nSequenceNumber ] ), + nSequenceNumber ); +--- a/rwcstring.cpp ++++ b/rwcstring.cpp +@@ -235,7 +235,7 @@ + + nMaxLength_ = nDefaultLengthForConversions; + +- nCurrentLength_ = sprintf( sz_, "%d", lNumberToConvert ); ++ nCurrentLength_ = sprintf( sz_, "%ld", lNumberToConvert ); + + if ( nCurrentLength_ > nMaxLength_ ) { + // big trouble--might not even make it here--might segmentation fault +--- a/someOtherProgramSentACommandToConsed.cpp ++++ b/someOtherProgramSentACommandToConsed.cpp +@@ -89,7 +89,7 @@ + + char szLine2[ nMaxLine ]; + +- sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine ); ++ sprintf( szLine2, "# of chars = %zu %s", strlen( szLine ), szLine ); + + cout << szLine2 << endl; + +--- a/tag.cpp ++++ b/tag.cpp +@@ -466,7 +466,7 @@ + fprintf( pPhdFile, "DATE: %s\n", soDate_.data() ); + + if ( lID_ != nUndefinedTagID ) { +- fprintf( pPhdFile, "ID: %d\n", lID_ ); ++ fprintf( pPhdFile, "ID: %ld\n", lID_ ); + } + + +--- a/userDefinedTagField.cpp ++++ b/userDefinedTagField.cpp +@@ -64,7 +64,7 @@ + + void userDefinedIntegerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { + +- fprintf( pFile, "%s %d\n", ++ fprintf( pFile, "%s %ld\n", + pUserDefinedTagFieldType_->soFieldName_.data(), + l_ ); + } +@@ -119,7 +119,7 @@ + + void userDefinedPointerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { + +- fprintf( pFile, "%s %d\n", ++ fprintf( pFile, "%s %ld\n", + pUserDefinedTagFieldType_->soFieldName_.data(), + lID_ ); + diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/consed/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest new file mode 100644 index 000000000000..81152dbf720b --- /dev/null +++ b/sci-biology/cufflinks/Manifest @@ -0,0 +1,9 @@ +AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 SHA256 284c120453ec82ed194cdff6cd6344ac9fcf3dfba9c960483313be077241838e SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a WHIRLPOOL a984c72436d307ecaf68efa5e6367d377912d616c4f35625df2471361a02ef2009d0f5d42355ac856852a3d30ecd390a1e9916bc67496df23637ebd5e6914afa +AUX cufflinks-2.2.1-flags.patch 1132 SHA256 3f86cd6ef757bc597bf4a511c119f176d4bb1bc06b3098791849446329f42a2e SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12 WHIRLPOOL 40db49fef766bf43508fc9748b31dce0098fc2cbd330106dd8156ccab39bbad5f5d15027fa126b6fe7eae082a10355319cca1b223e170d3ab99b8f587a8d935f +AUX cufflinks-2.2.1-gcc6.patch 344 SHA256 eb3df22fac5dc390ee72fcb2d1dd794d744acc08456a37d6343ead6348bc7786 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0 WHIRLPOOL 3bb3f042c3f1d2e9c3c58a57ef7f519063241f6526dc4ac464a7668d8ad41aff19d4b7e1a945f45ce28bab886bf7081d13a95fe423458442146d2894361d8c8a +AUX cufflinks-2.2.1-samtools-legacy.patch 1105 SHA256 384370accab11dee8b3bfa6f31a6e506bf6b1f1c82906d4d72194f58dd69b453 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf WHIRLPOOL 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2cc7d3924bf6276b0e748203ad96af4fc70fd52a61f05bb12b38bbb61b09ac1d51834260e5240fb1079253ccd05099f326961b2e3c8907209d40d114fadc1a81 WHIRLPOOL d892bb756e9b707829b709330a67b3ef7c550d3c7bfa34b0ab7eac49cd6ce7dda103e74c464d3592832b91f9cb880160c99ec2e90e4f47aa09f1e8e3707a8aa4 +MISC ChangeLog-2015 2124 SHA256 a1c5876fc85bd35681d61a2f8679365f556de35dfec2e9605e18b0e0016fabef SHA512 ed23958452e90447dd9f58c8bb2ab65d367bd44cf74f09ea00840a40afb3ba1c97c2df888bde5e46c05ed96cce7e2a54bdce0d491928dd0c1d01a6872c88036b WHIRLPOOL 3d087552cc441da6d0ae23f1532e04a79e7aa8862088d74079fd823f26e66a806637a56f547b8f674d5a602d160c1ab51157772bd726f765e0373141154c437d +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild new file mode 100644 index 000000000000..89f8484fad6a --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools flag-o-matic python-single-r1 toolchain-funcs + +DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + sci-biology/samtools:0.1-legacy + >=dev-libs/boost-1.62.0:= + ${PYTHON_DEPS}" +DEPEND=" + ${RDEPEND} + dev-cpp/eigen:3 + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-samtools-legacy.patch + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-gcc6.patch + "${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch +) + +src_prepare() { + default + python_fix_shebang src/cuffmerge + + eautoreconf +} + +src_configure() { + # keep in sync with Boost + append-cxxflags -std=c++14 + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + econf \ + --disable-optim \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \ + --with-bam="${EPREFIX}/usr/" \ + $(use_enable debug) \ + PYTHON="${PYTHON}" +} diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch new file mode 100644 index 000000000000..42a906e7a83a --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch @@ -0,0 +1,14 @@ +Boost 1.65 removed the TR1 headers. +Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654 + +--- a/src/biascorrection.h ++++ b/src/biascorrection.h +@@ -15,7 +15,7 @@ + #include <vector> + #include <list> + #include <string> +-#include <boost/tr1/unordered_map.hpp> ++#include <boost/unordered_map.hpp> + #include <boost/thread.hpp> + #include "common.h" + diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch new file mode 100644 index 000000000000..47784088fab9 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch @@ -0,0 +1,28 @@ + configure.ac | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 96ffbac..e88b8e4 100755 +--- a/configure.ac ++++ b/configure.ac +@@ -61,7 +61,8 @@ AC_CANONICAL_HOST + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024" ++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized" ++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024" + ext_CFLAGS="" + debug_CFLAGS="" + #echo "${host_cpu}-${host_os}" +@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with + [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" +-CXXFLAGS="$CFLAGS" +-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" ++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}" ++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" + user_LDFLAGS="$LDFLAGS" + LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch new file mode 100644 index 000000000000..6ee9bcf456d4 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch @@ -0,0 +1,14 @@ +--- a/src/lemon/error.h ++++ b/src/lemon/error.h +@@ -67,9 +67,9 @@ + } + + ExceptionMember& operator=(const ExceptionMember& copy) { +- if (ptr.get() == 0) return; ++ if (ptr.get() == 0) return *this; + try { +- if (!copy.valid()) return; ++ if (!copy.valid()) return *this; + *ptr = copy.get(); + } catch (...) {} + } diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch new file mode 100644 index 000000000000..374ce519ef86 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch @@ -0,0 +1,44 @@ +Modify the buildsystem to work with the legacy version of samtools, +which can coexist with the most recent version of samtools. +See also: https://bugs.gentoo.org/show_bug.cgi?id=577854 + +--- cufflinks-2.2.1/ax_bam.m4 ++++ cufflinks-2.2.1/ax_bam.m4 +@@ -102,7 +102,7 @@ + + AC_LANG_PUSH(C++) + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ +- @%:@include <bam/bam.h> ++ @%:@include <bam-0.1-legacy/bam.h> + ]], [[ + ]])],[ + AC_MSG_RESULT(yes) +@@ -171,7 +171,7 @@ + + AC_LANG_PUSH(C++) + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ +- @%:@include <bam/version.hpp> ++ @%:@include <bam-0.1-legacy/version.hpp> + ]], [[ + ]])],[ + AC_MSG_RESULT(yes) +@@ -189,7 +189,7 @@ + AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) + fi + else +- BAM_LIB="-lbam" ++ BAM_LIB="-lbam-0.1-legacy" + AC_SUBST(BAM_CPPFLAGS) + AC_SUBST(BAM_LDFLAGS) + AC_SUBST(BAM_LIB) +--- cufflinks-2.2.1/src/hits.h ++++ cufflinks-2.2.1/src/hits.h +@@ -18,7 +18,7 @@ + + #include <boost/shared_ptr.hpp> + +-#include <bam/sam.h> ++#include <bam-0.1-legacy/sam.h> + + #include "common.h" + #include "multireads.h" diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/cufflinks/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest new file mode 100644 index 000000000000..fd6ef56d4789 --- /dev/null +++ b/sci-biology/cutg/Manifest @@ -0,0 +1,5 @@ +DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93 +EBUILD cutg-160-r1.ebuild 1250 SHA256 59e602274fd15e923603bb7c4f0c8f1a09048b136773adffcd03c71d129958eb SHA512 4b7e71b255def1ece36d75ac85aa39e82b9e224317631801731fa0621e4841b00f6aa830e1fc43bb7e74fb387a2663c3848d9e0a5f99f550778448ab571ccacf WHIRLPOOL f3bded2d09f31650ff2c92b38a1dd91030c094ee29251d154d136d831413e88dd0a036b4b8f87fe2dbe9061cd584a310de0d80169327b4dcab51f05d919e6deb +MISC ChangeLog 2445 SHA256 d883f2b9bd991a0972e5739d3b89bb6dc47deeb4a3564c5fadae3c6a6054b732 SHA512 6dcbd245ade5394b4060b89833986d887e53d4d2fee8ac4f8f1dd705d900385922604a54ce45b4eabfe1997a2ac2b22a6cf08f52151f1b384372d13e2429ca35 WHIRLPOOL ae0770ac8aba3b6ca2701f2dbdc6593dd12b590d6dc6913455d1b6262d1545dafa9a8065b9cb534385fba353701ae258cbbb64d144094ef9a80df1d436562337 +MISC ChangeLog-2015 7744 SHA256 8723977349cf96250cecdefadb05bbe8270822b5baffbc477ca5a476792ce8fd SHA512 b365d6eb0563c1cdcd118e9efb1a1d12cec87fb6404f7161c9f43ecddc01523ec8dcfe0903887aca928893a32d5daa9987c15362892588b39dff4e14dff03673 WHIRLPOOL 178caf9920cb8f7b99c026196301bdaed6a42ffee61fec64d265b3aa752942adaa4d67877f62b7792ac63877aa9192cc892b27410311b1a221775c3cf397f75c +MISC metadata.xml 608 SHA256 215bb030a1c392e7e84bd43d2df7e8e2452223df44165544fbb88e97cecf8d76 SHA512 cf8142c4e77b18076f1916311ef85d9fac5d85c2b2139923c0bfb2ec5c8cae9d40d5f09c17128c531c850d726ba30f94b20c92415cb75f05e8f1d829f751d6eb WHIRLPOOL 3116cf5de61304c4a3034385a0cb3f20770026f400fa79dff9ed4a4030633fb876af51963dcddf4f9133070fdea9d2657fe355490664396cf0429baa0badc3b8 diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild new file mode 100644 index 000000000000..9a8130969019 --- /dev/null +++ b/sci-biology/cutg/cutg-160-r1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="Codon usage tables calculated from GenBank" +HOMEPAGE="http://www.kazusa.or.jp/codon/" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + mkdir CODONS || die + ebegin "Indexing CUTG for usage with EMBOSS." + EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \ + "Indexing CUTG failed." + eend + fi +} + +src_install() { + local file + dodoc README CODON_LABEL SPSUM_LABEL + if ! use minimal; then + dodir /usr/share/${PN} + mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \ + "Installing raw CUTG database failed." + fi + + if use emboss; then + dodir /usr/share/EMBOSS/data/CODONS + cd CODONS || die + for file in *; do + mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \ + "Installing the EMBOSS-indexed database failed." + done + fi +} diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml new file mode 100644 index 000000000000..d91990ea170f --- /dev/null +++ b/sci-biology/cutg/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + Codon usage tables maintained at the Kazusa DNA Research Institute. + Codon usage in individual genes has been calculated using the + nucleotide sequence data obtained from the GenBank Genetic Sequence + Database. The compilation of codon usage is synchronized with each + major release of GenBank. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest new file mode 100644 index 000000000000..4c873ae49621 --- /dev/null +++ b/sci-biology/dialign-tx/Manifest @@ -0,0 +1,7 @@ +AUX dialign-tx-1.0.2-implicits.patch 776 SHA256 c13bfae6c2ffa4a676fc92a1dbe7f82d08578e5f36add057d0ad84a955aa7ca5 SHA512 632da19c24834f011778e1be23a8b19f64da4e52386c99838393f678e927174bd8d3d9d175716e2651fcb884673123136166c401d3e687b882e5eaf69d597a1b WHIRLPOOL d5fd29ad957ffc734d4ef24811e3f131f86bfa2ffd4bd41da4353fd10f1a3a370e6ac531a943ded7fe908b89373e32e857d478e80453889e41aa1d102db272ea +AUX dialign-tx-1.0.2-modernize.patch 6149 SHA256 9556d6429018450214d2f49b0f148b380fde11575bcbc3f465e495fa130d9903 SHA512 cf1c1200500eb3e5f159468fe52536e8ffff60de21e09bb81e585270224ac4ce93d59fe80bd5a8212a4154ad90b23ec415be11b42792440c7fd53f75762d047a WHIRLPOOL 56d6ddaa0e2c62afdae05f11fcf8323bdb6b9b75a8e3a34c3e409395a8447de5c18e418dfae541fed2df7b045785ac81459f16ced912cfb0422839b2e2eda202 +DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277 +EBUILD dialign-tx-1.0.2-r1.ebuild 998 SHA256 83df32036d359ea01946b576ddb43a7dc0bd748387a410dcd8c147494ef9ac6b SHA512 7baa791bc863006cf66828bf3a08ec87afe03f72ba181280f5e26cf826a939bcc854bb94b40551f11a818006dae3a229db15f61b09f11438dece536e150b0ad0 WHIRLPOOL c140d4c566db4ae8b8375de58191031ee9d85d2ef3a1923df198d812c3782dc956c879dd6593653d4ce628e73aba90063fea28f676ccf55905b9366064160464 +MISC ChangeLog 2711 SHA256 ea9068d9b980f212b36e963cfb776cb7cf1aa819cb084833b92eff4a4d8f5b96 SHA512 f96f8e77c48085ab00ab16ef442db74808d5088b8626e08ad02ef2c292c9500fd2a9c8bfcd8c13bda264c36d5609e60afea0f9e270e9dcf685dd897362082bf9 WHIRLPOOL e3aff32f3dbe71b1e769bb251d761371d2d60ad39fc3523e36fadac6f378037e412aeae21a6e72ceec6e171a77cc51ad22a5370a6ec9137059d39d19926cac14 +MISC ChangeLog-2015 2455 SHA256 826243159ec72a293d7fdd92561bfa034991227eb8cff363a272dec0211c2986 SHA512 f36fbf5567d04ed9b3880480136a1524a562160d4cd8c6092c4df7a0ef05d3ddde9e483016dbc32f60ca2de5706f9bd2c0a77464c1ffe767d7f4a9e636533dd8 WHIRLPOOL 873a2d1aa9ff64633684ef3195909e92ef0a2d3d6ff4dcb4c1a828c4d0511eea82e93f03c5e660e4116e83135eaca59f369d88c0344831c871319ad8c2f1081f +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild new file mode 100644 index 000000000000..2f63ea80bb45 --- /dev/null +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +MY_P=DIALIGN-TX_${PV} + +DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment" +HOMEPAGE="http://dialign-tx.gobics.de/" +SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \ + -i source/Makefile || die #336533 + epatch "${FILESDIR}"/${P}-implicits.patch \ + "${FILESDIR}"/${P}-modernize.patch +} + +src_compile() { + emake -C source clean + emake -C source CC="$(tc-getCC)" \ + CPPFLAGS="" +} + +src_install() { + dobin "${S}"/source/dialign-tx + insinto /usr/$(get_libdir)/${PN}/conf + doins "${S}"/conf/* +} + +pkg_postinst() { + einfo "The configuration directory is" + einfo "${ROOT}usr/$(get_libdir)/${PN}/conf" + einfo "You will need to pass this to ${PN} on every run." +} diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch new file mode 100644 index 000000000000..a8388d03232f --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch @@ -0,0 +1,18 @@ +--- source/museq.c ++++ source/museq.c +@@ -38,6 +38,7 @@ + //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + // struct prob_dist *pdist); + //extern struct diag_col *create_diag_col(int seq_amount); ++extern void free_diag(struct diag* dg); + extern void free_diag_col(struct diag_col* dcol); + extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, + struct prob_dist *pdist, +@@ -52,6 +53,7 @@ + + // alig.c + extern struct alignment* create_empty_alignment(struct seq_col *scol); ++extern void free_alignment(struct alignment *algn); + //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); + extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, + struct scr_matrix* smatrix, diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch new file mode 100644 index 000000000000..b732e34da81c --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch @@ -0,0 +1,130 @@ +Fix changed gnu89->gnu11 inline semantics with GCC-5, Gentoo Bug #570252 +https://bugs.gentoo.org/show_bug.cgi?id=570252 + +In addition, fixed multiple -Wformat= warnings, such as + +io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=] + while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) { + ^ +io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=] +io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=] +io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=] +io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=] + +--- DIALIGN-TX_1.0.2/source/alig.c ++++ DIALIGN-TX_1.0.2/source/alig.c +@@ -10,9 +10,9 @@ + + extern void error(char *message); + extern void merror(char *msg1, char *msg2); +-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist); +-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ++extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + struct prob_dist *pdist); + //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos); + extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, +@@ -520,7 +520,7 @@ + * datastructure (i.e. frontiers). The given diag must be consistent + * to the given alignment ! + */ +-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { ++char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { + + char alignedSomething = 0; + int i,j,k; +--- DIALIGN-TX_1.0.2/source/assemble.c ++++ DIALIGN-TX_1.0.2/source/assemble.c +@@ -10,9 +10,9 @@ + + extern void error(char *message); + extern void merror(char *msg1, char *msg2); +-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist); +-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ++extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + struct prob_dist *pdist); + //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos); + extern long double** create_tmp_pdist(struct prob_dist *pdist); +@@ -22,7 +22,7 @@ + int n2, struct seq* sq2, unsigned int sp2, + int dlength); + extern void free_diag(struct diag* dg); +-extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, ++extern struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, + struct prob_dist *pdist, + struct gt_node* n1, + struct gt_node* n2, +@@ -34,10 +34,10 @@ + + extern struct alignment* create_empty_alignment(struct seq_col *scol); + extern void free_alignment(struct alignment *algn); +-extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); ++extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); + extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc); + //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); +-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ++extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); + //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand); + //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg); + +--- DIALIGN-TX_1.0.2/source/diag.c ++++ DIALIGN-TX_1.0.2/source/diag.c +@@ -183,7 +183,7 @@ + * omitScore = 0: normal + * omitScore = 1: no score calculation + */ +-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { + + if(dg->multi_dg) { +@@ -302,7 +302,7 @@ + } + } + +-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ++void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + struct prob_dist *pdist) { + real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); + } +--- DIALIGN-TX_1.0.2/source/io.c ++++ DIALIGN-TX_1.0.2/source/io.c +@@ -267,7 +267,7 @@ + for( c=r; c<length; c++) { + // check whether it is a regular acid or a special character like '$',... + if( (r<length-additional) && (c<length-additional)) { +- fscanf( fp, "%i", &is); ++ if( fscanf( fp, "%i", &is) ){}; + } else { + is = 0; + } +@@ -279,7 +279,7 @@ + // ensure symmetry of the weight matrix + data[length*c+r] = is; + } +- fscanf(fp, "%s\n", rline); ++ if( fscanf(fp, "%s\n", rline) ){}; + } + fclose(fp); + +@@ -368,7 +368,7 @@ + } + for(scr=0;scr<=mxscr;scr++) { + dist[i][scr]=1.0; +- fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ++ if( fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ) ){}; + //if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename); + scr = tscr; + if(weight==0.0) weight = 1.0; +@@ -532,7 +532,7 @@ + sdcol->data = malloc(sizeof (struct diag*)*alloc_size); + sdcol->length=0; + +- while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) { ++ while( fscanf(fp,"%i %i %i %i %i %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) { + if(sdcol->length >= alloc_size) { + alloc_size+=16; + sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size); diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/dialign-tx/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest new file mode 100644 index 000000000000..4a12bd78fd3a --- /dev/null +++ b/sci-biology/dialign2/Manifest @@ -0,0 +1,5 @@ +DIST dialign-2.2.1-src.tar.gz 209015 SHA256 046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 WHIRLPOOL a6c5cd25e8e1f3d3738ae0a7f9eaac2509a17400cc3492b9b0b5991c08df08b586c003bbaa3f92d22ae8dd13a66488e6acbbce0aca798cfd20938cb391a02f84 +EBUILD dialign2-2.2.1.ebuild 756 SHA256 047164b9db779d98c2a6fe56ed20b81a86afd50cb0a0fb13d407eddbdfef851c SHA512 ead9440fc5b4bbbed8ca6b6dd39ac57dfe8da4d2556c864ecddaf2b2f94589c95fd5fe82fc6ce45cab11eb8a197324b5cc89d38b0ca2c4f10741c3639799bbc3 WHIRLPOOL 465fedc6a149ac469e64536ac39a83aadbb9980dc9e608e693a9828d0422934eef5b4dd6e88a55a18eac44f7d5ee7fa4e0f6b73b04f75e7543533e7123e667f6 +MISC ChangeLog 2573 SHA256 94d2f159736a197045fc1107eaf8d604877170e26b6b7f98ffc2f0000e646801 SHA512 777987e0620df6e88903922d5effd3e2bdcef1eeb46c1964c822f6ca40dcfa9fbe9a15d93c6f721493758a30843b5875a13e2ca5c99a6287d30a0066c8f0a7fc WHIRLPOOL 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000000000000..13ce733d8a79 --- /dev/null +++ b/sci-biology/dialign2/dialign2-2.2.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Multiple sequence alignment" +HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" +SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/dialign_package + +src_compile() { + emake -C src \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -I. -DCONS -c" +} + +src_install() { + dobin src/${PN}-2 + insinto /usr/share/${PN} + doins dialign2_dir/* + + cat >> "${T}"/80${PN} <<- EOF + DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/80${PN} +} diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/dialign2/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/diya/Manifest b/sci-biology/diya/Manifest new file mode 100644 index 000000000000..db33b6914d41 --- /dev/null +++ b/sci-biology/diya/Manifest @@ -0,0 +1,5 @@ +DIST diya-1.0-rc4.tar.gz 386706 SHA256 13f7dd4dd7f96143948587884954e337552d7491347c2c174e786824880590c7 SHA512 64a00cb7f07200882d0b97f58e6b7f26d08ab0eab43834c3d19ab08f61080f8edb4a63833095e876c72c087324d39b2c4334ed1d3aa0280b7efb6a7ab3e08007 WHIRLPOOL 3efaf61a7e4129f1d3766b768dbe188df1c41d3158f431280022f17a8899db63b4db9a9774e48b49807e211ce58f28d588ebbd3037c8af5967b72e8e18539ffa +EBUILD diya-1.0_rc4.ebuild 1217 SHA256 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+SRC_URI="mirror://sourceforge/diyg/files/diya/diya-1.0/diya-${PV/_/-}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="-minimal" +KEYWORDS="~amd64 ~x86" + +DEPEND="sci-biology/bioperl + dev-perl/Data-Utilities + dev-perl/XML-Simple" +RDEPEND="${DEPEND} + !minimal? ( + sci-biology/mummer + sci-biology/glimmer + sci-biology/trnascan-se + sci-biology/infernal )" + +# see ftp://ftp.ncbi.nih.gov/blast/ to check if blast and blast+ are different from ncbi-tools and ncbi-tools++ +# * rfamscan.pl v0.1 (http://www.sanger.ac.uk/Users/sgj/code/) +# * UniRef50 (http://www.ebi.ac.uk/uniref/) +# * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/) +# The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/. + +S="${WORKDIR}/diya-${PV/_/-}" + +SRC_TEST=do + +src_install() { + mydoc="INSTALL README docs/diya.html" + perl-module_src_install + insinto /usr/share/${PN} + doins -r diya.conf docs examples scripts +} diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml new file mode 100644 index 000000000000..37bde911b940 --- /dev/null +++ b/sci-biology/diya/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">diyg</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest new file mode 100644 index 000000000000..127cef1fa218 --- /dev/null +++ b/sci-biology/elph/Manifest @@ -0,0 +1,6 @@ +AUX elph-1.0.1-fix-build-system.patch 1303 SHA256 5f1212cfd7fac3d15c969eee62fe9423c5d609a29a75a9f8cd599236fb188ba8 SHA512 d39611f80cd2e67e94f3d1dd7eb1dfe59ac3b221956ab72f3951b5716825387e7d3ed04608e75abfc43ae2cbc53ace474e602ddbd93441c2da74f04516ba2ba5 WHIRLPOOL 86dace4f513f6f0b41621e58ac783224916bf84031bed1223bc43566217b3474153814a9e023b7b9812e7f3ea63ade97bef8ed4d7da201440d0e0fab78e8d654 +DIST ELPH-1.0.1.tar.gz 113476 SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72 WHIRLPOOL 598dc3f95c93e5e36bcd20de3c985c22d650462ab27df31af54ca5b5b50c0a60fcc47637a41c449bdf7e572cee097289916aca4f0de79b804854d233ff3e20ff +EBUILD elph-1.0.1-r1.ebuild 658 SHA256 2843414d1f6279497e5577d0dfb9c8c2d32d3238fbc8f75336d23174948ba176 SHA512 ae25927fb71058c7543083735082e025defb746ea89f633e0bfa99291507e3a59ccdb05f51924b62a393dbaa40e727e83e83dc6e88b3acbe8e368cd856bd4121 WHIRLPOOL 4a84c71f80348508d1c6b825467da7f3a5df8f09d2e749fa4bcac972645dafcae8d26d3678f0b65283b00f14c696ef9fcb9998f0c7d2cc07e052e1e9d44b84d5 +MISC ChangeLog 2531 SHA256 d80ad382c93ebf13e79e3e0a159157d34bc781e995b42be22e3b850bed8c8f98 SHA512 2042496398adafd39319f7867c612a820275b984f825eaaecc3723468defa3aa0fd2f29613095fe13a844120d994493a78e861b1197a087ecae43e58ca7fe7c2 WHIRLPOOL 321afb35bca0963738f488b39bc6eaed74f3727763c826eef2094463937fd94abb3b2140c5c9e1df110fce9cc8bff767a1e53e30b48ea5851e252fa401a3c80e +MISC ChangeLog-2015 2410 SHA256 8f02ff022a059a9636b9d5fccb171cceb654c973c343eaff4dc5bc853d5634e6 SHA512 238c2d7ff81cfae365e2488bc5cb617af65b2f539f53c3e60fc1084302b578df46066ef60496f6c33265d97d0df526ed50fc6dbb8444c15913a8247f089f28bc WHIRLPOOL 808a8e0b99fde5bc1a2434bbf705a758e64faa7bbc876ac019ff71e62d14f819c3374323b50a707dc63f1f77c3f035c4aa3dabf4011a38a4fc79c25f1969374a +MISC metadata.xml 617 SHA256 577bac45e9296a2f04abd14bc8849a994b15f133958ecf4247a371dff4e25187 SHA512 d1998f0590fd4c555dcea00c1865da9258ba2a98bf7a1779703aca47ae01523cad74866e90fa612d16193c3974226519d4f5768180a3ae0646af2eb9fcbd1c2c WHIRLPOOL 82ff4415edbf7177606a2931079c0e0b137c91d5ed514f2fbf137eb112c82368bc66defd419a7ae5aa3c450ce986f0a7acb26ed5e10b89a188548bec049db887 diff --git a/sci-biology/elph/elph-1.0.1-r1.ebuild b/sci-biology/elph/elph-1.0.1-r1.ebuild new file mode 100644 index 000000000000..c166dd93e41d --- /dev/null +++ b/sci-biology/elph/elph-1.0.1-r1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" +LICENSE="Artistic" +HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +S=${WORKDIR}/${PN^^}/sources + +PATCHES=( "${FILESDIR}/${PN}-1.0.1-fix-build-system.patch" ) + +src_configure() { + tc-export CC CXX +} + +src_install() { + dobin elph + + cd "${WORKDIR}"/ELPH || die + dodoc VERSION + newdoc Readme.ELPH README +} diff --git a/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch b/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch new file mode 100644 index 000000000000..9afbb68666d6 --- /dev/null +++ b/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch @@ -0,0 +1,55 @@ +Make build system respect user variables + +--- a/Makefile ++++ b/Makefile +@@ -1,42 +1,26 @@ +-CLASSDIR := . +- +-# Directories to search for header files +-SEARCHDIRS := -I- -I${CLASSDIR} +- +- +-SYSTYPE := $(shell uname) +- +-# C compiler +- +-CC := g++ +-CFLAGS = -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -D_REENTRANT -g ++my_CPPFLAGS = -D_REENTRANT -I. + + %.o : %.c +- ${CC} ${CFLAGS} -c $< -o $@ ++ $(CC) -Wall $(CFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@ + + %.o : %.cc +- ${CC} ${CFLAGS} -c $< -o $@ ++ $(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@ + + %.o : %.C +- ${CC} ${CFLAGS} -c $< -o $@ ++ $(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@ + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ $(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@ + + %.o : %.cxx +- ${CC} ${CFLAGS} -c $< -o $@ ++ $(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@ + + # C/C++ linker +- +-LINKER := g++ +-LDFLAGS = +-LOADLIBES := +- + .PHONY : all + all: elph + +-elph: ./elph.o ${CLASSDIR}/motif.o ${CLASSDIR}/GBase.o ${CLASSDIR}/GString.o ${CLASSDIR}/GArgs.o +- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES} ++elph: elph.o motif.o GBase.o GString.o GArgs.o ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ + + # target for removing all object files + diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml new file mode 100644 index 000000000000..979dde87e15d --- /dev/null +++ b/sci-biology/elph/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + ELPH is a general-purpose Gibbs sampler for finding motifs in a set of + DNA or protein sequences. The program takes as input a set containing + anywhere from a few dozen to thousands of sequences, and searches + through them for the most common motif, assuming that each sequence + contains one copy of the motif. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest new file mode 100644 index 000000000000..ad9e72cf33d4 --- /dev/null +++ b/sci-biology/embassy-cbstools/Manifest @@ -0,0 +1,6 @@ +AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 3167 SHA256 8b73cb6b96e5afb0baced7ac7259addfb67b684d3c3035fa195f800bb264f08c SHA512 0ec7317d719da5466f02813105184d44c18f5ec668e0cdc1e120324216070009da4e38ce34dffb320b438665926f4506437e60757c3103fb03a526c46ca042d8 WHIRLPOOL ce99924dd94eee2df05665c8760efa2f9f2d374c896c526a0383875028e750f950004e79959c257aeecf750265fbd6b996de05b6fda7aa3a338e6d43cdf1672f +DIST embassy-cbstools-1.0.0.660.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a +EBUILD embassy-cbstools-1.0.0.660.ebuild 352 SHA256 04797dc5f89cdc030290c805d730a301ad72acdeb956a8e292abcb2b78a237e5 SHA512 f85c1ecdd7c16e13c8e1a08441b73a76f66ff770a3ca75eeb745f31b46aa5e2b74172f20de4b520e64e0ed167cf50b55d01ab78b760c9fbfde8ecee689f2703a WHIRLPOOL e41fadc600afcf81a49a4794f630d49bbbff49a6c5ab01c1a3453af074791e97f36b9d32b6cb5020a87c5055937431edf21b4e1d6cf70508aff33a9f94462308 +MISC ChangeLog 3712 SHA256 c3834418e0b0538c112851f6ccc138110748e0df3fa7f196a61c03508b862d1a SHA512 2f62c48e531025a873833d04af1585a19122b6648d0e6e3bb0db647043f48c76e04ed60562e2b877b51e9383884a75f4f218106fd19d7591f2c2a62c1cf8daf9 WHIRLPOOL 1b9a2e4a734599e52d586207e0c850747b450916dcd6774e9e1bb0550216a1a95a1b926feb60a076d001e9c751e77901fb5af0c5b41a089d1c2afb1d74246613 +MISC ChangeLog-2015 1799 SHA256 409f049c1e7d5031d8ddeeec23f2069e45b3e006a1098c24e07c2be2859bb212 SHA512 deb61b1a12f4790cab05ce0905cfb07e43648a9b38d914d10a4eeb6f5aadcc3a55b5a0291fe3df9bc5d2053a2ed838448d09d2b0bd6fdd62f714c0e62dc37f2b WHIRLPOOL 8e2256d7fcc4643b6108af8791f6ab7e362b97d89838954c596f0dbaf64a2dbd05c9c2e660f34372b88c8af33736ded26f91b111956797718e9d8c7a3aee24d2 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild new file mode 100644 index 000000000000..6104a470f3f7 --- /dev/null +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Applications from the CBS group" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +S="${WORKDIR}/CBSTOOLS-1.0.0.650" +PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..d29310efcb47 --- /dev/null +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index a70d4d2..b8f5e79 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 824a03c..9db171d 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -19,9 +19,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -65,5 +63,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-cbstools/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest new file mode 100644 index 000000000000..fd6bbeeca444 --- /dev/null +++ b/sci-biology/embassy-clustalomega/Manifest @@ -0,0 +1,6 @@ +AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2860 SHA256 21b6a87a19f37745f76fe9c45837d9a5bab6420dafcb9f50aa3899b88b3cd322 SHA512 6b1c8a2915c9c48ec203bc131461b9acecc3948da79f36941e2fd97a22bf044a35ee717e0be0b13f46d8a6f81148c29faa1e048ed4066cf768dbc705141a772d WHIRLPOOL 00b3a809502d22dfe01a3f5b12db5a62914753b81aaa4d4450c9506a1afcef65c9fa58706da6ca367de077395226aeb5ecb341cc5cb448aa0373a00569c9a778 +DIST embassy-clustalomega-1.1.0.660.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL 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2bbe112471e0e8042f170d73ac947b0d202cbbc86cefb596c97046bd1fd0319d15f24c17b99a6f69f8e1c346d44fa71ce039e0aee5e6829a8dc9b5c66e767ca4 WHIRLPOOL 99fe0031d3a5b19e5dfc757bb06764a705f063d0a71461cd735b04e95680b40ea9bc8a85f24b48fce2feb0228b96e3980a6119c3831ccf02c1f28a9942d17871 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild new file mode 100644 index 000000000000..2d2a2c62632c --- /dev/null +++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND="sci-biology/clustal-omega" + +S="${WORKDIR}/CLUSTALOMEGA-1.1.0" +PATCHES=( "${FILESDIR}"/${PN}-1.1.0_fix-build-system.patch ) diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch new file mode 100644 index 000000000000..5525d79b525f --- /dev/null +++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f12ed19..b143922 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9135679..c201149 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-clustalomega/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest new file mode 100644 index 000000000000..fc4349289add --- /dev/null +++ b/sci-biology/embassy-domainatrix/Manifest @@ -0,0 +1,6 @@ +AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2860 SHA256 e44b11ca5a40404db741838ce87a68c536723bb81b3729dc1ef021c050d59b7b SHA512 9c8dfdd2e6c7f8542a989118dad6c70159c55a7f56593800b9d1896fb717b0c28ea100f5884f3284823ad1e92da6e5fe307e798028475e29d353edfe52b62865 WHIRLPOOL b02d9f774e807bca06b4a16d1438a5970c412868309333f35b39db5c067821a30a37affc9b74b44c8dcd458969f9dc1aa4ad07835b9660020bf10f26ed421fd5 +DIST embassy-domainatrix-0.1.660.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0 +EBUILD embassy-domainatrix-0.1.660.ebuild 345 SHA256 da2c8c3ae8e45af225e9b28ae00ca3112aac955ccd21a1d55b3e4dd1488fd691 SHA512 0438a817780278fb85fbd6ba9135725e5b6a850318f8b8e95a504b388e649f7a19fc8472145ced331193d64addbaa1603c3c89e0272872f8795a13cf44d0288f WHIRLPOOL 130580891b28786330c204a7132386b7fbc8dd578a28fb05c14399f5a76840804dcff9709d7f535ff5c08bc4772a27e07e1f13cf2bebf56c42b96dd65258de33 +MISC ChangeLog 3740 SHA256 355fa6e17b11140fbb3bddb902bd9a089b9852abddadcec48092136a5bfbc619 SHA512 dcd955932cf92a35a24fe3afb5e9c69472108aeb13bae65349e81b89b82ae8f46f90a00e8d4834ea71e6c1ce4cf1e4f3ca13f9ccfff73f74682cbc7319a780f4 WHIRLPOOL 887058d56ab82ab7565a4e87cbc5b3df6e5d23a10a4402bade4e14a2acb1f10adfd8f509e95b66c18e1f958999b87e814b2000d1dc132d9eb6080748b20b1c1f +MISC ChangeLog-2015 5803 SHA256 519cb6863e78ea24aef1f05084802a891f4eef60ae9394eb7fa2c59fcda781c4 SHA512 1c79388eca11496a9d09b96de8324d4fc7041e7ee08a7813d8b81f1fc7084c808b348f2ebb3d3e66aaa948c23546ebdb16122aa2beedd58db1a077c2b9a88d9c WHIRLPOOL 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+EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/DOMAINATRIX-0.1.650" +PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..a932e1ebe21e --- /dev/null +++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index d16cc02..d327a0d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index d405d00..54be7ca 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -64,5 +62,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-domainatrix/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest new file mode 100644 index 000000000000..330ea4156ac7 --- /dev/null +++ b/sci-biology/embassy-domalign/Manifest @@ -0,0 +1,6 @@ +AUX embassy-domalign-0.1.650_fix-build-system.patch 2908 SHA256 3c4b3c8187942d52b5605f83cb2430cebb050fb7d6180e2784a041a4fe332d48 SHA512 5cd02b39812adc44d9b877cca8902b6a66e79c90975b50233a4f8f84392026ffad25d57665e68e5db533f28935f444b4dc75b7120bafd910e415b75737686ad2 WHIRLPOOL 0a7ddde136f33cb2618957ddfc5f7d7d62f1352e4902b700d1b22c636b0424bdbca28fb6946d97095d75ba5ce61b21b93647c10920ebe8e4539fba5751efca32 +DIST embassy-domalign-0.1.660.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37 +EBUILD embassy-domalign-0.1.660.ebuild 343 SHA256 af35754f603a88b67066c06f5d740c70558110c4a2d8e46eea840243c11880bf SHA512 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emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/DOMALIGN-0.1.650" +PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..033ddf7b6535 --- /dev/null +++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch @@ -0,0 +1,101 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 ++----- + 2 files changed, 9 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 693eb4d..dc0fda9 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 8785446..fe85f11 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-domalign/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest new file mode 100644 index 000000000000..b57c08dbe610 --- /dev/null +++ b/sci-biology/embassy-domsearch/Manifest @@ -0,0 +1,6 @@ +AUX embassy-domsearch-0.1.650_fix-build-system.patch 2890 SHA256 8b6901b6126ec5642c08ff114b2401d2b498b6912e2c58e0767156d775d0a166 SHA512 3f012a5646751b43ec66d006df04cbe8fa880d0acd62723962dbb0e1817c5f5db2bd4879c25cf932114aa43291bc70816afef6664088532222e11135f0ab5603 WHIRLPOOL 11cb26d3dcab609c43d404afaeca56f44439fe84bf4d25b05bdd98c4838e11d19753f2f3390af93c7d9b9141226e02804190cd8a8f0061dd7d67bd0e0d989644 +DIST embassy-domsearch-0.1.660.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111 +EBUILD embassy-domsearch-0.1.660.ebuild 341 SHA256 3e25fee23debf35e06c6e2c1a1f1d31f1913d7a2782165fb86d71f60da8111d1 SHA512 b7719faa5c0b7fd20379351f41930926cdea99e5c1b26e23aec3f7aceae12e1db885997782b2c4ca89e0bc5d92e17261e990d644ba04da36d9c219c0e5732afa WHIRLPOOL adc45d6d31b88003d7395fd1dd570b1f7ae90dd68015bb83d02431f8a929c54e51cc8681febff2b3b387ed20f26c3b7283627f1b0bcdf4ec3cfd06a903419103 +MISC ChangeLog 3722 SHA256 a46008601cf02935daa424c5201e812f1e86c00db5ff3325ff9853a7c16a10b7 SHA512 4116820109aa24ceca048ebe8875aff64095991a881d8d9026b86eb84736df6bc9b7e4d3015b32d6da2a5ea1baed072ff78a515246efc176e2f52dcbd71e72f7 WHIRLPOOL 22dbd4538aa426a57006b95a340f00e7a2e2b101d340e2bd3c4ab04f2ddf91e61e8139a7c243f7c63c4343a1a2fdb82e0e1fee0c0cacae15a261c86ced661dcd +MISC ChangeLog-2015 3869 SHA256 bd705086afad7fdfa6045c3d7fca59e2b3036b2d65d2a43585e1add5bb13cd58 SHA512 0914a10689fc1d3d6e44cdfe75158e275b56362a700aec1ba2ab7ceaf4e6e212d5881c7fa38ee774da39e5d858d44574ff625c2996b03d6843453703d298184c WHIRLPOOL 03fbac60078932d22105d1c3b113ab5acc1cb916da773efe0cd2fada41b1ef5d686c8208135168e327749a2102a7d9c77a01c21bd1d2360dc1e52185bd51746c +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild new file mode 100644 index 000000000000..a47adcfb8457 --- /dev/null +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Protein domain search add-on package" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/DOMSEARCH-0.1.650" +PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..d24857c8386d --- /dev/null +++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f0f97fa..d419d7d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9829ebd..433a5c5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-domsearch/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest new file mode 100644 index 000000000000..6bc01d894564 --- /dev/null +++ b/sci-biology/embassy-emnu/Manifest @@ -0,0 +1,6 @@ +AUX embassy-emnu-1.05.650_fix-build-system.patch 4072 SHA256 fe36162b0925c6b2746d6663c91853cbdf964c42ab950fb5613506518d1cac15 SHA512 644c4f0930a157ae9121354b49ddeb756b25d823d25733405fcc500d2080067f013443ba43a1512c6940fc4fd19cfe38c336dd0c58237354bad580cf9ba68b2e WHIRLPOOL 36dd5eab9ad368e471fbf799443a4a0d8132b89e31f670b030735f768684d4afe21577962c3ae0476f949c116a514425a16345edfb8172548df156b61b0cd1ff +DIST embassy-emnu-1.05.660.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a +EBUILD embassy-emnu-1.05.660.ebuild 470 SHA256 b4d1cdbdb92f508690a3f20e6e9931022c9942460bf996f1fdeb4b07f9bf8103 SHA512 ec9df242ed5a421fdbc45b59c1a9a9a3cfe540bde2ea010a29ac56e758d26fa0f1a1c850de644e82486a574850b0702d7d87adebfd851cd40076e17596c88f05 WHIRLPOOL f040dee96571b9ebbb3d9c4c73873b9020acb657dba9e1c0492b90c7319f5aa3fe88db34bed269cecf6bfc3de07c3a9480b6c4487432e440eda3250ab3da483a +MISC ChangeLog 3890 SHA256 b80d3323420fe549f7f0de661fcd6fbd323999f4f5904cf19d511123b321230f SHA512 dfdb5b23e58614ecc42d9cd39e66b3113816d53dfc820a7ec5422bfea9c433a9fb89102e996e066f57a465b0f7accb43288986671da403fb3700032cd408d2cb WHIRLPOOL e28af714bc0a187135230cc876001549b6c181d92ecc1ab133ed3e6618cc4d75df4bc422631ffe324624d9a797c55b8564520158b3403c6514f086e0c42a5d5e +MISC ChangeLog-2015 5221 SHA256 c23b8feae038f5de8eb63d9f0f6c569b0acc03e25cebd2c9b5bfd4c7e45d0967 SHA512 34da4783348408202dbc240d9fdcbc370ac0385c1b41be4a73e9c565e25f84633b808525980edbdd47ec1a2f0f31cc03369d9208d340e4653de86cc8a90ab4c3 WHIRLPOOL 0047620191be27d41e3f7ed9d86b1e733b136379b8e263701b5fcc03f35fdd47bc511d26ca60b7e8b7b73aacd9b2bd0242875202cbc712a049189a87a9f8e8fb +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild new file mode 100644 index 000000000000..fd6b02d8d235 --- /dev/null +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Simple menu of EMBOSS applications" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" +IUSE="ncurses" + +RDEPEND="ncurses? ( sys-libs/ncurses:0= )" + +S="${WORKDIR}/EMNU-1.05.650" +PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch ) + +src_configure() { + emboss-r2_src_configure $(use_enable ncurses curses) +} diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch new file mode 100644 index 000000000000..4e14bac1704a --- /dev/null +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -0,0 +1,139 @@ + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 7 +++--- + 3 files changed, 18 insertions(+), 58 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 7482ade..b815bdb 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -899,20 +864,16 @@ dnl fi + + + dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +-[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) + +-AC_MSG_CHECKING([for curses]) +- +-AS_IF([test "${with_curses}"], +-[ +- CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +- LDFLAGS="$LDFLAGS -L${with_curses}/lib" ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++ PKG_CHECK_MODULES([FORM], [form]) ++ PKG_CHECK_MODULES([MENU], [menu]) + ]) + +-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"]) +- + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b295079..330c76f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \ ++ $(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS) + endif + + if ISSHARED +@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) ++ -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-emnu/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest new file mode 100644 index 000000000000..ed7c101c46c4 --- /dev/null +++ b/sci-biology/embassy-esim4/Manifest @@ -0,0 +1,6 @@ +AUX embassy-esim4-1.0.0.650_fix-build-system.patch 3167 SHA256 25d191cabc62f3651e7f0cd999573b788827a2f3fb75e5c7be7716797c511577 SHA512 c8f4468998b1e91122e4ee5f355c5db451fa889892c05125edcc2f734051410251de85a9d7aaf5566dc802240d2925c709cfd448c8f96351aaa91c124eb1396f WHIRLPOOL 1558f5aca98ef8e6742c5990e7bb604d99ff80d6994147e01e2b1a3afc1c50e5efb56b9649d228da90bd955c83e3e12b65cfdc45c3bd50667de0c4236229be6b +DIST embassy-esim4-1.0.0.660.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62 +EBUILD embassy-esim4-1.0.0.660.ebuild 345 SHA256 894db7ee83fc1895dc4a40318eba1e1e456d310afabbaa5f8a73b31f8061fbfc SHA512 baff9c211e98de225f8644a441b99b4693f16068c151b5ee5b59c481e6de564e5cce0f0617bdb52a3d96b642a3b22dd558eab3329098d3ac028527818dc16357 WHIRLPOOL 10d85eeb74a687704d2f542f11be349932f60bc3ae3d9a89896584a9961404ffce8e1ade74dc14d202b0122f764cd0b45af8f50adc458a066a08e07c6418c799 +MISC ChangeLog 3694 SHA256 cd070895ae878ac17a3e6e434ba823e1e4a5ed6930be5e89e7be98bc16caf30a SHA512 61189ae9edf9e4e3c6795f43909217448921e9a384aec01e90700b29c3453718ea689e130dc42d4082c2b0f9173f769393d94b63fc09e7f356d4cf8f482d4cb4 WHIRLPOOL f5d96dfb32b04b068131b8c20c53a851f106803d1ba0d427bd5f452f1e726343fc8e47982f45ff87ea24d10bc86a3bdc827ea577008d0599444ab9dd345d245f +MISC ChangeLog-2015 5174 SHA256 97faf62dbc69f607804fe3204629293bd24a994c4ec0aa4fdcb437b5e427d180 SHA512 daa106d334327da2c13cbf74b4c4269e9fe2510ad1d1fcf67b7d9a90c51c972e608ad6434d531babe5af21cf18aa660d5cc779bcbcd6d9544b212e30846caae1 WHIRLPOOL 8a7780dfcf6a58321e586ba240eae5b0706d96244ba351e05be0a62ea87b2599758b68bd459264cb03e4d0502e555e93597ff0811e6b7420d52e8769be466e3c +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild new file mode 100644 index 000000000000..16b6d29ebdaf --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/ESIM4-1.0.0.650" +PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..ead54c91b5f3 --- /dev/null +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 924220a..2c45f46 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 0620938..0304bb8 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-esim4/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest new file mode 100644 index 000000000000..3e16dd3c9ae4 --- /dev/null +++ b/sci-biology/embassy-hmmer/Manifest @@ -0,0 +1,7 @@ +AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2860 SHA256 6d05b00b1fa6946594cb3e5dea4e3d1652decab49bcb5313801d8ed4a33e51ac SHA512 f215e5c338aa1f0bf791de223f3ee9a13622f70e142c5ad4812dfe171f7d602aab750e1dfe4233324752adc645abf289e63d8981b8497787c785c07de64c7944 WHIRLPOOL 19d3b640de27436d40b95c451c0d39458b1f4a69eed7cb536e7417606d792dea91c677e719cde5b82873060549f36794ec6f36ba71a7549d619fe7f645d8fa62 +AUX embassy-hmmer-2.3.2.660-slotted-hmmer2.patch 3392 SHA256 d2ccf44c1f012300b7578553d697a950714c0eb93cf630799d16b662951f73da SHA512 18d1595b7cd6091917f9657310b286d2f0d1f6a61c045840b1c551b66162142997b837cc50b47a3a5fa7efec4ffa78e5b9b52804e3c4d41efeed9b4edb6e5507 WHIRLPOOL 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6632a1ac5d0fba8f1e0e9fe844e366120f360bb50ee7fcc48921f1c43d272a7c SHA512 2ec9e47acbd20102d2041c75376ef8b65781bd8593a9d5d3a866a9981e97bac5ecc32ad5b8272dea4db9a1106c94db35515169e5ca9c890459c2a4829d0953fc WHIRLPOOL 783eb072d06f81c664d86f20fa2165190310f9714b82bbb5b1eb72cdae7096c26dee4104ae7f5098671e82693fc098c961dded8826d34cf50148ae650271c2a4 +MISC ChangeLog-2015 5450 SHA256 f37958058bb7d3d532c9970a9aaa2f146fd9da610aa362e8e697b6aa4811150c SHA512 ff79da3b23f057604319a93af4e3b50b72d293abf6d4441aacac3e0074fc8fd4ce9027cfe26529c0555238bb5091fe75d2c4f24d7f1cf8ee8feea4438bf1eda9 WHIRLPOOL 2a9bfb84467181d90356468d17387a8fb21cabdf0c533239e1152ec61d34b3454d5097678e794303e479419282efc1bb005af03ef2dd4d59e70da7b751f025cc +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild new file mode 100644 index 000000000000..4fa2defa1f7d --- /dev/null +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND="sci-biology/hmmer:2" + +S="${WORKDIR}/HMMER-2.3.2.650" +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2.650_fix-build-system.patch + # sci-biology/hmmer:2 has renamed commandline program names + "${FILESDIR}"/${PN}-2.3.2.660-slotted-hmmer2.patch +) diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch new file mode 100644 index 000000000000..90c45632eada --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 037ca00..f539ab6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index dc789bc..5a8c38e 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch new file mode 100644 index 000000000000..f202ddf3d0b5 --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch @@ -0,0 +1,101 @@ +Amend command-line names for Gentoo SLOTed hmmer:2 + +--- a/src/ehmmalign.c ++++ b/src/ehmmalign.c +@@ -99,7 +99,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign2")); + if(mapali) + ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali)); + if(withali) +--- a/src/ehmmbuild.c ++++ b/src/ehmmbuild.c +@@ -146,7 +146,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild2")); + if(prior) + ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior)); + if(null) +--- a/src/ehmmcalibrate.c ++++ b/src/ehmmcalibrate.c +@@ -98,7 +98,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate2")); + if(cpu) + ajFmtPrintAppS(&cmd, " --cpu %d ", cpu); + if(fixed) +--- a/src/ehmmconvert.c ++++ b/src/ehmmconvert.c +@@ -72,7 +72,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert2")); + + /* ACD option only allows one selection */ + option = ajStrGetCharFirst(format); +--- a/src/ehmmemit.c ++++ b/src/ehmmemit.c +@@ -79,7 +79,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit2")); + ajFmtPrintAppS(&cmd, " --seed %d ", seed); + if(a) + ajStrAppendC(&cmd, " -a "); +--- a/src/ehmmfetch.c ++++ b/src/ehmmfetch.c +@@ -74,7 +74,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch2")); + if(nhmm) + ajStrAppendC(&cmd, " -n "); + /* Note the output redirected to outfname */ +--- a/src/ehmmindex.c ++++ b/src/ehmmindex.c +@@ -68,7 +68,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex2")); + ajStrAppendC(&cmd, ajFileGetNameC(database)); + + +--- a/src/ehmmpfam.c ++++ b/src/ehmmpfam.c +@@ -122,7 +122,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam2")); + if(nuc) + ajStrAppendC(&cmd, " -n "); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); +--- a/src/ehmmsearch.c ++++ b/src/ehmmsearch.c +@@ -102,7 +102,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch2")); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); + if(compat) + ajStrAppendC(&cmd, " --compat "); diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-hmmer/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest new file mode 100644 index 000000000000..fa29a4858056 --- /dev/null +++ b/sci-biology/embassy-iprscan/Manifest @@ -0,0 +1,6 @@ +AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 3167 SHA256 4ee85226fda51d4232bbce8c8f1f3d9b6deedb794864bb16c13eee514ad49b09 SHA512 b2b28377e60790db744f32eb5cd4de5b7e15129b603e21013eeeebaea5c06e6867937b6441f3d8e788effdbb58c57b8841880aa7d4b4eae2b0b83dc72242f4d8 WHIRLPOOL f7e9084619cc6b0b1e8425753e5f44ab41b22d309afe10e3a01eab67eb76258cebe3b6ecad340d247f6ca51bff0a1fac4f2125a8f8be5e30466b50fdee3ee494 +DIST embassy-iprscan-4.3.1.660.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8 +EBUILD embassy-iprscan-4.3.1.660.ebuild 363 SHA256 38f3fe16d5752340814d336e4c2152d3fb7e116ca2e1d889145af9754768726d SHA512 3b140b4b5f4e25d6935b4f159cf636d76dd5437c97fa3c4d0293287db5e1e52cda7db29eb4a0cd4b34aa9596da791725a51a653af27be52cdfbfb76c6ba1c1f6 WHIRLPOOL e80ec1b503269314457ea219e256061cace3775b3fc6293f33bb527932356d4bbc0445f9551b00f420b1c053a8bb99bd54d6d933c5f64a7219c1693f57fde9a1 +MISC ChangeLog 3703 SHA256 0e8e02ef4ddbf82293585913d79f0f614cccd638cd177b915f07ff93b3620d0b SHA512 a184d73c14b908ff8acfde1cf9592a8420682daec138c278fe3c7ead6fab9223028aa29a784471b40912414689f60e5b3d401d2cd6d8d2a5b55a82c77957ac40 WHIRLPOOL 8953578b043bc0f80b039529337eac4f0beb08bf915fcc7e92efa142fd20aa6e8972bff943435928a36939adbd1feef4cbdf419494ae998e9534676be388616f +MISC ChangeLog-2015 1781 SHA256 015954d5dfc1ad4daa5ba6b0f4492b754cae024770b6a03fd1d4c55ae280a24a SHA512 2022d1f98a55d9f57600c6a9f7fef6bfc8a15678bce2b3d6b3531be7c532ae31f27e0b7626b180b39e5eca29cb581973eab307666c7819fead2b3f8047ba45ce WHIRLPOOL 42f145f36c3be160be823dc14c7ccd4ea831c569000064306a73b5cd87b367520545e16c1d0954ea0a379a32b9cc968625d33fc510e49a30ff49321a07e2dd1f +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild new file mode 100644 index 000000000000..3279ed3bc8e8 --- /dev/null +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="InterProScan motif detection add-on package" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +S="${WORKDIR}/IPRSCAN-4.3.1.650" +PATCHES=( "${FILESDIR}"/${PN}-4.3.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch new file mode 100644 index 000000000000..8c8a1060e30f --- /dev/null +++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 9052ca5..c12c268 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 0afc96a..904b41a 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-iprscan/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest new file mode 100644 index 000000000000..5021cd8b5caa --- /dev/null +++ b/sci-biology/embassy-meme/Manifest @@ -0,0 +1,6 @@ +AUX embassy-meme-4.7.650_fix-build-system.patch 2860 SHA256 928eb90afbc7b70f69fd4bb7f1090bbd4ea2bd3d7a286b56c947dd481156b5b6 SHA512 c44b219c75e67d17fcfd56145ae3709053bda38b8690141d1e9b846e4e4a9cab135f0dc9c5399e4712cf030ad562dd075f45c393e78157a2c1b92d80903b3d1c WHIRLPOOL 4e93c672ee6026ee7b2e2ff6c8771a375049629f5e24e2e6cf9afa72cced5fc62d21f49c161fb5ffe55f0637ffe14baf78df15c1c95e0a42d3495a1619365141 +DIST embassy-meme-4.7.660.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 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0b079723cd9c0a825cae54d654e4ccc7f051242ec7eb399de0265e2ce43960b57d7854825535a2300a0b96ac70d735b6d23fe086a13192108b14addd4f3605c0 WHIRLPOOL af77519eb83320b982ed520d1d2b7a81edf88d4971a731c8964bca1080c2c4a9b4202a1f16addd68bca4893699a08b4419bc504fb34a4e0552d809646f272bd9 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild new file mode 100644 index 000000000000..8752e78d8fc9 --- /dev/null +++ b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="sci-biology/meme" + +S="${WORKDIR}/MEME-4.7.650" +PATCHES=( "${FILESDIR}"/${PN}-4.7.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch new file mode 100644 index 000000000000..56f5814e1efa --- /dev/null +++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 391989f..d921f25 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 1600399..9f28162 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-meme/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest new file mode 100644 index 000000000000..d64545ddc9c6 --- /dev/null +++ b/sci-biology/embassy-mse/Manifest @@ -0,0 +1,6 @@ +AUX embassy-mse-3.0.0.650_fix-build-system.patch 4274 SHA256 599b095e98864d4268b5959517c1002b3b591a45d865e42f409eb0059af5168b SHA512 bfb4663a4b38928f765813cc9b5e773ca712c2333c1650d9c78f457307aa450684f77a20c0a087d3795d5b51f059c6f8113e74da35aa78753c1cc666ba583f4b WHIRLPOOL 418dc60bb9cf2023d499eec13b132f1aaab7bd9538ba2bc12f3f19926a25f7e7f0fb3b9b99e80acddfb57a4762aba5c90e413ffe5c8aa05d593d1309ecc28db8 +DIST embassy-mse-3.0.0.660.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b +EBUILD embassy-mse-3.0.0.660.ebuild 563 SHA256 95486ba509879ea87d6f2a7a97987b22857881181cb3fa0046299a45cc4bf20a SHA512 80cc7b8c36d5675f8f4caf9fb244ce1b2740bef6813c4f62e4084a07f31d173abc0fbc4b486e7fda12b701ffe9d99efb023e76fdceaf29c87c2b5182ea1609f9 WHIRLPOOL 422b7ce3a899e1260da66c78c5e763e986e438a9b9ae3ece5cd23cd5df516f395ebd0971563f505189d9a2a5d0cf03db03442c7ce8d05e1e083a0d197ab8a86a +MISC ChangeLog 3557 SHA256 63d5d3e0ceb7785312a8ac18c6b3a6e7fd4569f0dbf7f9192d1684f403428e57 SHA512 ebad0d05b2493db898c50a6e1d268313da3d60705159dff3cef1f388d6a249bd7cb9e7c9e7a0639d99969316eb680a9d10be21935bc067bc70f758b6627d1671 WHIRLPOOL d4dd277affb7666a0380d0e3890c88a8f25725bb92fcc6bd81b0b866bc5234530cd6d3759732cf41014e6ea7a82fca160b7e4f2fd5190ac6aa60c8e924b2725e +MISC ChangeLog-2015 6196 SHA256 33d5a20ceaea1924c0fc21af8053c9e4fd1385a6b352c4224c9ec6de563041ba SHA512 29895c8f1db31e3fb946dfbf95ba737530fd9eeecca7cab5713075f06cc0a4c3e647df72369cefc3023a8ef36f2aeaa2677158431e44239d8517fa7257403281 WHIRLPOOL c520584027ef2ffef27609a3388c995c90160a90c9039f5d88414e9a5c46c85c24fb3bd9f4af24e694de1320d05d065fd2d08108344be05aa2c8de965cc38471 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild new file mode 100644 index 000000000000..c22970155918 --- /dev/null +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.660.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" +IUSE="ncurses" + +RDEPEND="ncurses? ( sys-libs/ncurses:0= )" + +S="${WORKDIR}/MSE-3.0.0.650" +PATCHES=( "${FILESDIR}"/${PN}-3.0.0.650_fix-build-system.patch ) + +src_configure() { + emboss-r2_src_configure $(use_enable ncurses curses) +} + +src_install() { + emboss-r2_src_install + + insinto /usr/include/emboss/mse + doins h/*.h +} diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..c1095b266d60 --- /dev/null +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -0,0 +1,149 @@ + ckit/Makefile.am | 2 +- + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++--- + 4 files changed, 18 insertions(+), 59 deletions(-) + +diff --git a/ckit/Makefile.am b/ckit/Makefile.am +index f87b131..a670d2b 100644 +--- a/ckit/Makefile.am ++++ b/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +diff --git a/configure.ac b/configure.ac +index a20d488..eb208bf 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"], + + + +-dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +- [AS_HELP_STRING([--with-curses], +- [curses (or ncurses)])]) +-if test "${with_curses}" ; then +-AC_MSG_CHECKING([for curses]) +-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +-LDFLAGS="$LDFLAGS -L${with_curses}/lib" +-fi +-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) ++ ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++]) + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b44632a..84e89b5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../h -I${embprefix}/include \ +- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ +- $(NLINCLUDES) ++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \ + $(XLIB) + else + LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-mse/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest new file mode 100644 index 000000000000..49cbaae159f1 --- /dev/null +++ b/sci-biology/embassy-phylipnew/Manifest @@ -0,0 +1,6 @@ +AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3255 SHA256 26aad2bc72f89444dffdd301cfd4f50ba582b10082f21153e601c6812075ba86 SHA512 a0d4dcb3e7d4ce9b5cbd68168ebe7c8d248aa1166a6a52a0a77031291af8d2d32af0243571b669b9318426f753251d983ebb9b96eb1da81b594f4f4d20d7c249 WHIRLPOOL de7d91731115bca913a65a8f4a44d863433338ea4e5acb7f6a9fefca9a185325b18888d8339d180a49ecb7dfeb91f120a7c7188fe23f340dd21aeb8b3940458e +DIST embassy-phylipnew-3.69.660.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58 +EBUILD embassy-phylipnew-3.69.660.ebuild 360 SHA256 f709676a2f9165b6fc0463fa866887b346306b71b99659ab8888922a29395e16 SHA512 cadc029f641b4303325f4d4110a130bc46b1e74b2c6246bb31cc07ff2bd8801adc6438cf2253897d3d6c28bf4fd6f9bad098b73d0e664b79bec5899157551e12 WHIRLPOOL ad40e021462a8ee0ada38eae9d4be237ea154889b20d584f498a5b8fe96575f434f62fa298f4b985422bfa7c152b929c8781ac1db9acdb26e1b91d5bb116270f +MISC ChangeLog 3713 SHA256 16e0941c89aebf00fe14bd00989a743873ac62b951e97cb76f0351d92b87899a SHA512 5184a0b1a6f8e989c0eece6b2b1dcfcfd7c4ef0bcddf9cb25eab69d7eef104c0807b72390d29e5f7ab909a3c9fb224af24f649b3d28f711b1aa4e20f2ece08a7 WHIRLPOOL 0958d0036cbf66b26b46fc41287c62f56c3499b2d66d7fd174ee30ac7a9088c9afec662803c41626fd4ab87101d58b7a57da78e27f3e771234ccb5b9a7ceceee +MISC ChangeLog-2015 2806 SHA256 142f97be3bcc2cfe360418a11835c21109505aa7085b705e93832b586ce957f9 SHA512 5d9859ac63566d082fb58bb3eb6ca81fce1bcdab06624e7795dcec6f28564c33c87f7b62a642e153c1a1f161cb995ad52b04cf2fed8029d3e5afdd28948135f6 WHIRLPOOL ad62b40aca5b1d875cb26944dcbcbc7f288024e298c3c0d1868e1a72074995bfa3b0ab40c8e7e6686bab57c11e85c013e4826d474a178803e65d6fe0172d0dd4 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild new file mode 100644 index 000000000000..69834a313b8f --- /dev/null +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="The Phylogeny Inference Package" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +LICENSE+=" freedist" + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/PHYLIPNEW-3.69.650" +PATCHES=( "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch new file mode 100644 index 000000000000..1cba944094a2 --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -0,0 +1,111 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 7 ++----- + 3 files changed, 10 insertions(+), 48 deletions(-) + +diff --git a/configure.ac b/configure.ac +index e5bfaf1..09ed517 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 1883ce9..fb1787f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-phylipnew/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest new file mode 100644 index 000000000000..70ea7d7dabe5 --- /dev/null +++ b/sci-biology/embassy-signature/Manifest @@ -0,0 +1,6 @@ +AUX embassy-signature-0.1.650_fix-build-system.patch 2860 SHA256 768fe1c2740827007d475f31451195090032b907e0ed5b36b9201504d6eb4df2 SHA512 54a6027b2fb1d17eff98b7c1e9adc61578a2845b30be3b7c40551b4291950ce11900798dbf7d54e1fc9421743a8d313fc42a14cfa39976735ac8cfae5a297954 WHIRLPOOL a272e7679d14c883fb76d83e78e429582c776364c590738f4bb6b3e793f54c95bd0bb42b263fc6ca5569a34a9be2e84a2dc62cb67efe05ad451ac0513102c2d8 +DIST embassy-signature-0.1.660.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3 +EBUILD embassy-signature-0.1.660.ebuild 337 SHA256 f6f54e84e70866656557e64974fc3d6773e9c62a3541e4e94e254446e14cdafa SHA512 ce592d367c64428911a735a5ecc3a24000a5b1e8c3b3fcaf466e5005a962deaf113416cd161039eb445a1a41f7296ca7376531396bed019047c0d97c86296585 WHIRLPOOL f0c8b7d716026c97fc01f50ece571de4d13c522832c1e2f65aa1f57cc7ac0a3ada05ded0996f2822e31141cf5be19779ae4c928ef947c6e7749145775d8be929 +MISC ChangeLog 3722 SHA256 535090c557eb13db1501c464a1ca480e81081ac6a447d8f9b60898fff0aac43f SHA512 21cf306716bc2071f5344c7e7a89380eaaeb696d4689fcc4e26844f50f0ab170806cee5949896d6365a86f21dbdf16517e6eec6c03720726192b3ec58b685d62 WHIRLPOOL a4e86701782c8a8f9f557d979f9d6ea383df0c95438843623b295740aa81776af5af7c3314374aa76c08e936e5e511b20c9198a1090bbebaf4ff7af5270b4428 +MISC ChangeLog-2015 3864 SHA256 27b743af18ee8d2fc1420f1dcb7aba01c65211fb4c7ac965a2926f141fa8428a SHA512 220fd9e7da3a4c4a306631d4460b39431de1e5d29af32257071e0cb35c680541eea139825c5bfe1760e7313df2b4695b2cbe7850fe2fc916f3cb50c66cfd50e3 WHIRLPOOL a1596d167902201f0fc6f735186372d6c0f5de529106f524af11bfb8de08e9d1dc518a0984936c4873f03d062a43b6e5a168ea2eba10a16edcaf83cced3fdfd1 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild new file mode 100644 index 000000000000..c0ea3e302504 --- /dev/null +++ b/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Protein signature add-on package" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/SIGNATURE-0.1.650" +PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..32e4d684cbb3 --- /dev/null +++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 2f5ddd0..827543f 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index d77e43c..849f17a 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-signature/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest new file mode 100644 index 000000000000..6f97607adee6 --- /dev/null +++ b/sci-biology/embassy-structure/Manifest @@ -0,0 +1,6 @@ +AUX embassy-structure-0.1.650_fix-build-system.patch 2860 SHA256 e8d2923a0cc2eeeb97ed731afb6922fca203887e1b3570d0e46910065db86ca6 SHA512 8929ee9e2eff5636e4d40ec5d1860d866e90c17cc23f4e75f44fd829409591b869cd5feb13a6c02bb5d80a9a7ed55c06f7be45f61268a768ddfdafe84188237c WHIRLPOOL 80f9e14144f20bbf64863804b28fe6fca2a7856d868d5d43ac612e0ab9d3d655a979734ae77c97c3ac4903bf577a3384bc0041d0b4c69faa03bd41edb3fa8e44 +DIST embassy-structure-0.1.660.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03 +EBUILD embassy-structure-0.1.660.ebuild 337 SHA256 f26b1a6676d2c48cb8305cafaa7cea8a8f0d493b3f50aebbef031087f02704de SHA512 13a68a4590058e36d0ee5e016bfdae8e2115aefdec8d50ff988b0841f6bc1cc210c090da97811c4aaf654e132f32b28bdca559dcf157d7a3a0a66a2dfc946c3d WHIRLPOOL aac75fa870806b87b861cdf3c7471f9d3238db859ba7786f02c05029990ff88829bf8c1d518e5d01f686e434170b21fb67f4a174e71545a3f4ee894e381b66fd +MISC ChangeLog 3722 SHA256 7862433f0ae9699bf7f3556c0078a17e43608fe0d2914ef483d92fd05aa9e9df SHA512 64aa480179e8f71e6c2bed04b52758f4d2e64c613be7d4ad16b36600153c13987fcb06d4a0b0c937366262c7838145c65a708be0730acecb19da745bd519607c WHIRLPOOL 7421edc569bc9d73364c8edc5d594ce116c1f14aea40d437976a87a6e2b3ef3204b4ff583a658ffb11edaf1cf00c17669d3139a0aa350cd7d702a1aaa78ced77 +MISC ChangeLog-2015 3898 SHA256 5fe31e03f1c5d75ff9606b6d89fe311de8692e7c97ae3ad7cc9924e46cba5f7d SHA512 6a3f1667263fae6eca976b85eacba15d71121087e6d9803c0bd995c2cb3986c6c33e02f274c10a1c88ed3fd206dde4456b49be0f663866c07dd256a0de8469be WHIRLPOOL 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emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/STRUCTURE-0.1.650" +PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..bdd9e37714e4 --- /dev/null +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index ee482ef..e4af4b1 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 81ade5d..2ed0d14 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-structure/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest new file mode 100644 index 000000000000..a1f17bf5ac50 --- /dev/null +++ b/sci-biology/embassy-topo/Manifest @@ -0,0 +1,6 @@ +AUX embassy-topo-2.0.650_fix-build-system.patch 3167 SHA256 d78bcacee455ab12fdb482fa760eb89716da3bac9dbf5ace0f9bba37f2585dbf SHA512 bacff621e9d80d39a4e415736e1524cf69dd86b0253f65fb52ad2dda200cafe8e14af296897c3f695bbe360f2a56862a40dec6b8b0d0e597310f065e191ae770 WHIRLPOOL 09ffc786288a0b428f349cf74973729a9dea8d8ed2078897538b97b59ef41cd48053e0763c6665310a770c6410b28726fe9c09b0ada9543d6fd8054b1e99b24f +DIST embassy-topo-2.0.660.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55 +EBUILD embassy-topo-2.0.660.ebuild 342 SHA256 07b735f534f885f651c75d4135d45d15417fcb97340ff25cf4ba4e03612b7595 SHA512 c2a0822f7d20ae5c2bb78aa2f3705517fa7371b154a16395d7b13b5835980a11dce9364cb6d0a90f47a39cc729692b4567ceb5085022b3c0ed41535a3a8ab067 WHIRLPOOL ef6c670b13175f0f99d48aa7b978757c7ff1bf6e2984909f6ba8a48de5f4c2d79145c2dfecaf6e3a6f90dda93fbb7942ac38f6db69707e69bc943e8b0822c28f +MISC ChangeLog 3671 SHA256 7e5217f1daaad28f1c3c4137c619bbf5075360217fe9ad443a32c7a61e8e94fc SHA512 7399a29b68d4b9d974c463aed165882eb8ea32c48ae8297dc2856cea08d032db73579aec4d243f31032df947cd560cc00b6d7c17a3596b9edccca0f693d4f45c WHIRLPOOL d4c5cf7abeab2f3e68ef0c12e8eb48e2a76a653f07481fd9aea955a159c68eaa09dd86108b9181c3965eaf504c4fea191296a5142727926d864c61d718d66db7 +MISC ChangeLog-2015 5212 SHA256 9bf176f777b2a7325026c20377fe46465c1f29f96a1af3e78ac3721a511bb30f SHA512 c7c527494cba100183d37b40b97913f3b4d401de0d990ccc1bda92288deb994e25f8daac07ea14b18287435a3409ec81a489bdf2be333d21ace00db07f1835f7 WHIRLPOOL 05b8f8040075da4b7e2277547af92019562d3a744b7370c2e9dc98df7d43d36a3972e88ef96295831c95f23d0b2c4027ba3f6ceda25304699c4be490c2c06f3f +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild new file mode 100644 index 000000000000..009adfe73914 --- /dev/null +++ b/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Transmembrane protein display" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +S="${WORKDIR}/TOPO-2.0.650" +PATCHES=( "${FILESDIR}"/${PN}-2.0.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch new file mode 100644 index 000000000000..3c37879de8c8 --- /dev/null +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 8eeb8ca..4fd28ac 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 1cdb0b1..0e86a4b 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-topo/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest new file mode 100644 index 000000000000..7d8b7b7889e9 --- /dev/null +++ b/sci-biology/embassy-vienna/Manifest @@ -0,0 +1,6 @@ +AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3083 SHA256 0831ff5582301bb74750a5c4b7006b5ccfb7dfeeaa4c5772c051ed628715a390 SHA512 b09ea9adcc9da002a83e431ff4f3f48075bd885bd35b5690a21ed7d120835a5fa9eaf566fecfd916897e18d539ccc7ea1c8640759996e4979865556eaf8dccb2 WHIRLPOOL 1ca51a2336916b491eb26b846f0810d8ecd722ed9552c1faa83d360a94e8724cb50be3873788e67c05ef10368c43985fde61a61ecb765261195a4eab90289e8c +DIST embassy-vienna-1.7.2.660.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2 +EBUILD embassy-vienna-1.7.2.660.ebuild 436 SHA256 df9e13e427b920830067db610d4e1165d0f4adaa0e7970e04a83f7f5320960f0 SHA512 009ad16069bd0a8134a705a82a2d1ee5a3b5de28d434870e9b7298e64885a8c76f1c604432b2d0808d6f4653906e211b6c848496bbefd0c4324d698fb8285ec3 WHIRLPOOL b007cccee75f2b5ad1b2c8dfbe2a64cc510de3accc86c0419699303727cdd881ce190c97967b5e9d08218a13a699318909ffb99c5d892e2b355c506c3a56fe45 +MISC ChangeLog 3854 SHA256 b48b7425e67aa4ff49d83c33f50413c2d783f08d4b2426b6ea2d2c99f5d9509d SHA512 4ded7e01a2a4574c210d7de8baffed5a696489b6a6715fc75cba19c19c987593a5b600c2d24b535310f2f1364952a95eea77c75e540f4634aa09224cf15ceb69 WHIRLPOOL 2b2c4aa1ead8586d396b1b895574107300bbaa1d515ec1287431b74e45830d6998f16fa24ee0b1dcc741885749db8c3dfe00b40ea108e77b5651159c116ba5c2 +MISC ChangeLog-2015 2134 SHA256 4ce8df30009ff6337fa540ba1ad4ae9478c67968b46048a3dcb3ab2a1c2eb0b2 SHA512 55156fd3adf143e66a1f93578657c70ecd3e54134d238e07e094e2344b842bb8df0f5346eb8e7f92257e751f50b06e643c282551b8eed4a3eca661eb11dce810 WHIRLPOOL f24c077f90166fbec7400263a1b4016fb69576bf2c188238d4d60efdcf682a5b7da9c8237eef639ab90ec210a3f146edcc4297ab9065901c3a3646f84fdf2db1 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild new file mode 100644 index 000000000000..d82532a4f623 --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Vienna RNA package - RNA folding" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 flag-o-matic + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +S="${WORKDIR}/VIENNA-1.7.2.650" +PATCHES=( "${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch ) + +src_configure() { + append-cflags -std=gnu89 + emboss-r2_src_configure +} diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch new file mode 100644 index 000000000000..5ce365ed5497 --- /dev/null +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -0,0 +1,108 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 +++---- + 2 files changed, 10 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f5a4ecf..bbe0743 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -649,33 +649,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 1f5b756..e178914 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF) + endif + + liboviennarna_la_LDFLAGS = $(LINKFLAGS) ++liboviennarna_la_LIBADD = -lajax + + ovrnaalifold_SOURCES = vrnaalifold.c + ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c +@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \ + $(XLIB) + else + LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-vienna/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest new file mode 100644 index 000000000000..dd5d1c3c6332 --- /dev/null +++ b/sci-biology/embassy/Manifest @@ -0,0 +1,4 @@ +EBUILD embassy-6.6.0-r1.ebuild 967 SHA256 a74a8e9824f900ce6049af2d3a5a782a6f5f7ca859d9c753b346d9dc1617ba67 SHA512 028181280e723f6926b9a9ad2fba67f10fb2ce3e78ee9b9dfb5e07948d9b4c1db41c12ee4349794de6b99d2bac8021f856883d01466a5a6421a801eca58f74de WHIRLPOOL c266f5b860cbccbc3a9da7de1b7e22b2a85940e5889e10ce891ac55071b8bf2408b344f49b7391983d38363312a467ab641b1bb892c90b7cb84f6c50940f01ad +MISC ChangeLog 3560 SHA256 5f80df41c055924a1a115ac65050ffc3d7c38b17c1119be85d7adf1675cdd766 SHA512 54062925d52d802de9d076d956619ecb283f82bee2aeecf9f6a78abfff5d50ee4b56eeacfb201315fd4f480f4e4aee306058c90859a5c179d4e526bc9a72bcb2 WHIRLPOOL a9facc21af6eb698ab751c1c821de036e773e23eeecf2ef25179a3390e0ad732f97be78b9b35f308b3c018b4a18dcc1bcecbdc863e7ec8a2a5eb07b3fa4101cf +MISC ChangeLog-2015 5006 SHA256 c5af2d6800d77f862fb0bc5d0b8daa1c35e192d0b579924c756704b0e8d39008 SHA512 b712eeeb6ec48db9690223e4b694c2c0be25f375d01fd5d5f66d613470ecfc189820587c01f50f68fcd782daba62713ca4924687ecfd284d49b8767db954ff65 WHIRLPOOL 5b023359ed56184f3ecacd38ae306820e8d919fecc4e6c03de0aa4d8aea411d9694e6f45f9f3588797a70fb5e98d96ec403ee8bdfefa4f84737455c1917a2f01 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy/embassy-6.6.0-r1.ebuild b/sci-biology/embassy/embassy-6.6.0-r1.ebuild new file mode 100644 index 000000000000..27edbc3fd4f6 --- /dev/null +++ b/sci-biology/embassy/embassy-6.6.0-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" +HOMEPAGE="http://emboss.sourceforge.net/embassy/" + +LICENSE+=" freedist" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND=" + >=sci-biology/embassy-cbstools-1.0.0.660 + >=sci-biology/embassy-clustalomega-1.1.0.660 + >=sci-biology/embassy-domainatrix-0.1.660 + >=sci-biology/embassy-domalign-0.1.660 + >=sci-biology/embassy-domsearch-0.1.660 + >=sci-biology/embassy-emnu-1.05.660 + >=sci-biology/embassy-esim4-1.0.0.660 + >=sci-biology/embassy-hmmer-2.3.2.660 + >=sci-biology/embassy-iprscan-4.3.1.660 + >=sci-biology/embassy-meme-4.7.660 + >=sci-biology/embassy-mse-3.0.0.660 + >=sci-biology/embassy-phylipnew-3.69.660 + >=sci-biology/embassy-signature-0.1.660 + >=sci-biology/embassy-structure-0.1.660 + >=sci-biology/embassy-topo-2.0.660 + >=sci-biology/embassy-vienna-1.7.2.660 +" diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest new file mode 100644 index 000000000000..3e260fbd1307 --- /dev/null +++ b/sci-biology/emboss/Manifest @@ -0,0 +1,10 @@ +AUX README.gentoo 1522 SHA256 3cbb20ef948613f07698ab17c2b432e3aeab0ade6499a965c538d4feae8440d2 SHA512 a5441a056ebb11d24b83b8bfb9182f0753b85ec5ba126a123eb97c55fc665dadff2cc5f16c8e4314535f1b6a206c200324c0c5d5db6af109c841ee68ac76bb07 WHIRLPOOL b659d2c08416786ce4bdd0de0d61da49c1e6be4524e19c4b262a81a6455bf6b3e24ca0f1c7b5414c5fda35a006827fc5e229411821247b76bc26afda5a0a21d8 +AUX emboss-6.6.0_FORTIFY_SOURCE-fix.patch 417 SHA256 317bff2c29f321afe7274babba8db554420a26744cef6aa73885b18e7434e89f SHA512 9873504675825613c913fbd8c03d919c5d70ad7f15e3983ae9dc5ecd04e57d1086c303a4f38efd29def4f089099b24449014bbe965816c7f8b37a5d4ffa13469 WHIRLPOOL b23ea76326c732d5c25429589bed6301d0a6e9342523275a40c225c2af0e25eb2b6279905c52633b35eb3208bf43b7f4a1307c5f66bf95e81e8c8097d967d801 +AUX emboss-6.6.0_fix-build-system.patch 12599 SHA256 9ff77b03a1b1d5d28ae7720a6e61ddf226337d04aaf4da69e3c9a5918dcea7de SHA512 60dbb50967b0b855fabd68f2df7713da81007cb84aeb3f2d7510d13e533e3b19ed3d07e012010ebb1b2af04522f6f2142fbef405b9b580740a6bb5d30319b67b WHIRLPOOL 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7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe +EBUILD emboss-6.6.0-r1.ebuild 1648 SHA256 74dc9b874d2cd6a49e18b9f354c011e4ccffd2a256903115872d404a9ff55efb SHA512 3ff85cc699f9ccfaf68d8335b8631a7f976ad69e82a8bd0be70123fb61ab90c50250691c1e507b2ba891a07b5e6693612209d44780afe35ceef4e2c431f9d265 WHIRLPOOL 98bcab5a9f8c285d9c00d0c08784e060ac65913668dcd2bb36fa30e311c367454fb3b7610eeb233bd44a0b0314b53a8e8af65f6e297dc3d423191cf3b17514ce +MISC ChangeLog 5649 SHA256 6d655b59592dd57123b0bde406c08fcc5e4f63943e7918d4e24563f3bb55c9cc SHA512 1666627eab0475e700adef75869d76c0e5aa2fcb7a8487fecb9905dbc422b9272dac58f837c90aba126bda8f44dd6de4d4022d34ed0de987be10e35bbcec8645 WHIRLPOOL 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000000000000..2aa5aa9bc5c9 --- /dev/null +++ b/sci-biology/emboss/emboss-6.6.0-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_EAUTORECONF=1 + +inherit emboss-r2 readme.gentoo-r1 + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +SRC_URI="ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz" + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="minimal" +LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" + +RDEPEND=" + !games-action/xbomber + !sys-devel/cons" +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/primer3 + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + )" + +S="${WORKDIR}/${P^^}" + +PATCHES=( + "${FILESDIR}"/${P}_fix-build-system.patch + "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch + "${FILESDIR}"/${P}_plplot-declarations.patch + "${FILESDIR}"/${P}_qa-implicit-declarations.patch +) + +src_install() { + emboss-r2_src_install + + readme.gentoo_create_doc + + # Install env file for setting libplplot and acd files path. + cat > 22emboss <<- EOF || die + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" + EOF + doenvd 22emboss + + # Remove useless dummy files + find "${ED%/}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files" + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.gentoo". + mv "${ED%/}"/usr/share/EMBOSS/data/CODONS{,.orig} \ + || die "Failed to move CODON directory" +} + +pkg_postinst() { + readme.gentoo_print_elog +} diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo new file mode 100644 index 000000000000..d1879bd0811c --- /dev/null +++ b/sci-biology/emboss/files/README.gentoo @@ -0,0 +1,34 @@ +Administrating EMBOSS on Gentoo systems +======================================= + + +Codon data files location +------------------------- + +The codon data files that are distributed with EMBOSS are installed in the +``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual +``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between +these codon files and those installed with the CUTG database. The names of +these files sometimes vary only by their case. Having both sets of files in +the same directory is also impossible on systems such as MacOSX, where the +root filesystem is case insensitive. If you do not have the CUTG database +installed and want to use the codon files distributed with EMBOSS, you can +symlink the ``CODONS.orig`` directory to ``CODONS``:: + + # cd ${EPREFIX}/usr/share/EMBOSS/data + # ln -s CODONS.orig CODONS + + +Restriction enzymes equivalence file location +--------------------------------------------- + +The restriction enzymes equivalence file distributed with EMBOSS is installed +as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual +``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file +collision with the equivalence file provided by the Rebase database. If you do +not have the Rebase database installed and want to use the equivalence file +distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to +``embossre.equ``:: + + # cd ${EPREFIX}/usr/share/EMBOSS/data + # ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch new file mode 100644 index 000000000000..7704873e9d26 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch @@ -0,0 +1,11 @@ +--- EMBOSS-6.6.0/emboss/embossversion.c ++++ EMBOSS-6.6.0/emboss/embossversion.c +@@ -415,7 +415,7 @@ + ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); + #endif + #ifdef _FORTIFY_SOURCE +- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); ++ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); + #endif + ajFmtPrintF(outfile, "\n"); + ajFmtPrintF(outfile, "Sizes (bytes):\n"); diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch new file mode 100644 index 000000000000..266bddd95a37 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch @@ -0,0 +1,411 @@ + Makefile.am | 9 +++--- + ajax/Makefile.am | 4 +-- + ajax/acd/Makefile.am | 8 +++-- + ajax/ajaxdb/Makefile.am | 6 ++-- + ajax/core/Makefile.am | 6 ++-- + ajax/core/ajreg.h | 7 ++-- + ajax/ensembl/Makefile.am | 6 ++-- + ajax/graphics/Makefile.am | 8 +++-- + configure.ac | 82 ++++++++++++++++++++++++++--------------------- + emboss/Makefile.am | 13 +++++--- + jemboss/lib/Makefile.am | 2 +- + m4/idxdbs.m4 | 17 +++------- + nucleus/Makefile.am | 8 +++-- + 13 files changed, 100 insertions(+), 76 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 177dec5..18dd99a 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -12,8 +12,11 @@ LICENSE \ + ONEWS \ + PROBLEMS + +-SUBDIRS = \ +-plplot \ ++SUBDIRS = ++if !ESYSTEMLIBS ++SUBDIRS += plplot ++endif ++SUBDIRS += \ + ajax \ + nucleus \ + emboss \ +@@ -33,5 +36,3 @@ dist-hook: + tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + +-install-exec-hook: +- $(bindir)/embossupdate +diff --git a/ajax/Makefile.am b/ajax/Makefile.am +index f27472c..de34e17 100644 +--- a/ajax/Makefile.am ++++ b/ajax/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + +-SUBDIRS = pcre ++SUBDIRS = + if !ESYSTEMLIBS +-SUBDIRS += expat zlib ++SUBDIRS += pcre expat zlib + endif + SUBDIRS += core graphics ensembl ajaxdb acd +diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am +index 9f0f700..3295a1d 100644 +--- a/ajax/acd/Makefile.am ++++ b/ajax/acd/Makefile.am +@@ -3,16 +3,20 @@ + lib_LTLIBRARIES = libacd.la + + libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la + + libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics +-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++libacd_la_CFLAGS += $(PLPLOT_CFLAGS) ++endif + libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) + + libacd_la_LDFLAGS = -version-info 6:5:0 +diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am +index c2b0c00..9de14fe 100644 +--- a/ajax/ajaxdb/Makefile.am ++++ b/ajax/ajaxdb/Makefile.am +@@ -3,14 +3,16 @@ + lib_LTLIBRARIES = libajaxdb.la + + libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la + + libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl +-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) + libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) + +diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am +index 2906837..3189c34 100644 +--- a/ajax/core/Makefile.am ++++ b/ajax/core/Makefile.am +@@ -3,13 +3,15 @@ + lib_LTLIBRARIES = libajax.la + + libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) + +-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajax_la_CPPFLAGS = + if !ESYSTEMLIBS ++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) + libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) + libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 1623c82..5d928cf 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h +@@ -39,9 +39,8 @@ + #include "ajdefine.h" + #include "ajstr.h" + +-#include "pcre_config.h" +-#include "pcre_internal.h" +-#include "pcreposix.h" ++#include <pcre.h> ++#include <pcreposix.h> + + AJ_BEGIN_DECLS + +@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS + + typedef struct AjSRegexp + { +- real_pcre *pcre; ++ struct real_pcre *pcre; + pcre_extra *extra; + int *ovector; + const char* orig; +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index 0d1250b..5484c02 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am +@@ -3,13 +3,15 @@ + lib_LTLIBRARIES = libensembl.la + + libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libensembl_la_LIBADD = ../core/libajax.la + +-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) + + libensembl_la_LDFLAGS = -version-info 6:5:0 +diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am +index a4f202b..1114c2c 100644 +--- a/ajax/graphics/Makefile.am ++++ b/ajax/graphics/Makefile.am +@@ -3,12 +3,16 @@ + lib_LTLIBRARIES = libajaxg.la + + libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) + +-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat +-endif + libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) ++endif + libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) + + libajaxg_la_LDFLAGS = -version-info 6:5:0 +diff --git a/configure.ac b/configure.ac +index a7bd9c6..9ba3121 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -629,32 +629,6 @@ AS_CASE([${host_os}], + + + +- +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- + dnl Define where the EMBOSS package is located + AC_SUBST([AJAX_FIXED_ROOT]) + AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" +@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE + +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) + + + +@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs], + + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PCRE], [libpcre]) ++ PKG_CHECK_MODULES([EXPAT], [expat]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++], ++[ ++dnl using bundled libraries ++ dnl PCRE library definitions - see the MAJOR and MINOR values ++ dnl to see which version's configure.ac these lines come from + ++ dnl Provide the current PCRE version information. Do not use numbers ++ dnl with leading zeros for the minor version, as they end up in a C ++ dnl macro, and may be treated as octal constants. Stick to single ++ dnl digits for minor numbers less than 10. There are unlikely to be ++ dnl that many releases anyway. ++ ++ PCRE_MAJOR="7" ++ PCRE_MINOR="9" ++ PCRE_DATE="11-Apr-2009" ++ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" ++ ++ dnl Default values for miscellaneous macros ++ ++ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" ++ ++ dnl Provide versioning information for libtool shared libraries that ++ dnl are built by default on Unix systems. ++ ++ PCRE_LIB_VERSION="0:1:0" ++ PCRE_POSIXLIB_VERSION="0:0:0" ++ ++ dnl "Export" these variables for PCRE ++ AC_SUBST([HAVE_MEMMOVE]) ++ AC_SUBST([HAVE_STRERROR]) ++ AC_SUBST([PCRE_MAJOR]) ++ AC_SUBST([PCRE_MINOR]) ++ AC_SUBST([PCRE_DATE]) ++ AC_SUBST([PCRE_VERSION]) ++ AC_SUBST([PCRE_LIB_VERSION]) ++ AC_SUBST([PCRE_POSIXLIB_VERSION]) ++ AC_SUBST([POSIX_MALLOC_THRESHOLD]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss/Makefile.am b/emboss/Makefile.am +index 89ada78..f987d40 100644 +--- a/emboss/Makefile.am ++++ b/emboss/Makefile.am +@@ -28,15 +28,18 @@ endif + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd + AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb ++AM_CPPFLAGS += -I$(top_srcdir)/ajax/core + AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl + AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics ++if !ESYSTEMLIBS + AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre +-if !ESYSTEMLIBS + AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat + AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif +-AM_CPPFLAGS += -I$(top_srcdir)/nucleus + AM_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++AM_CFLAGS += $(PLPLOT_CFLAGS) ++endif ++AM_CPPFLAGS += -I$(top_srcdir)/nucleus + AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) + AM_CPPFLAGS += $(JAVA_CPPFLAGS) + +@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la + if !ESYSTEMLIBS + LDADD += ../ajax/zlib/libezlib.la + LDADD += ../ajax/expat/libeexpat.la +-endif + LDADD += ../ajax/pcre/libepcre.la + LDADD += ../plplot/libeplplot.la ++else ++LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) ++endif + LDADD += $(XLIB) + + #if PURIFY +diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am +index 5f7e21e..8b45ce2 100644 +--- a/jemboss/lib/Makefile.am ++++ b/jemboss/lib/Makefile.am +@@ -12,7 +12,7 @@ mail.jar \ + jalviewApplet.jar \ + jemboss.jar + +-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java ++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java + if JAVA_BUILD + $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; + endif +diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4 +index 0ca7ea9..9b54f2a 100644 +--- a/m4/idxdbs.m4 ++++ b/m4/idxdbs.m4 +@@ -1,17 +1,8 @@ + AC_DEFUN([CHECK_IDXDBS], + [ +-AC_MSG_CHECKING(for EMBOSS pre-indexed databases) ++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) + +- +-if test -f ./emboss/index/edam.xac; then +-AC_MSG_RESULT(yes) +-else +-AC_MSG_RESULT(no) +-echo "" +-echo "Pre-indexed edam, taxon + drcat databases not found." +-echo "Please download them from within this directory using:" +-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." +-echo "and then repeat the configure step." +-exit 1 +-fi ++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], ++ [], ++ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) + ]) +diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am +index 37b8543..5819c89 100644 +--- a/nucleus/Makefile.am ++++ b/nucleus/Makefile.am +@@ -3,6 +3,7 @@ + lib_LTLIBRARIES = libnucleus.la + + libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la + + if ISSHARED + if ISAIXIA64 +@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm + endif + endif + +-libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot +-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot ++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++else ++libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) + endif + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch new file mode 100644 index 000000000000..15f5f967a07d --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch @@ -0,0 +1,61 @@ +--- EMBOSS-6.6.0/ajax/graphics/ajgraph.c ++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c +@@ -49,7 +49,7 @@ + + #define GRAPH_DEBUG 1 + +-#include "plplotP.h" ++#include <plplotP.h> + + + static void GraphArray(ajuint numofpoints, +@@ -964,10 +964,10 @@ + if(!thys->ready) + { + #if GRAPH_DEBUG +- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); ++ ajDebug("=g= plsfnam ('%S')\n", txt); + #endif + +- plxsfnam(ajStrGetPtr(txt), ext); ++ plsfnam(ajStrGetPtr(txt)); + ajStrAssignS(&graphBasename, txt); + ajStrAssignC(&graphExtension, ext); + if(ajStrGetCharFirst(graphExtension) == '.') +@@ -1213,10 +1213,10 @@ + void ajGraphicsSetPenwidth(float penwidth) + { + #if GRAPH_DEBUG +- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); ++ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); + #endif + +- plwid((PLINT)penwidth); ++ c_plwidth((PLINT)penwidth); + + return; + } +@@ -1538,10 +1538,10 @@ + static void GraphSetPen(ajint colour) + { + #if GRAPH_DEBUG +- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); ++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); + #endif + +- plcol((PLINT)colour); ++ plcol0((PLINT)colour); + + return; + } +--- EMBOSS-6.6.0/ajax/graphics/ajgraph.h ++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h +@@ -32,7 +32,7 @@ + /* ========================================================================= */ + + #include "ajdefine.h" +-#include "plplot.h" ++#include <plplot.h> + #include "ajgraphstruct.h" + #include "ajdefine.h" + #include "ajstr.h" diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch new file mode 100644 index 000000000000..eff10b2e6700 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch @@ -0,0 +1,74 @@ +--- EMBOSS-6.6.0/ajax/core/ajfeatread.c ++++ EMBOSS-6.6.0/ajax/core/ajfeatread.c +@@ -45,6 +45,7 @@ + + #include <limits.h> + #include <math.h> ++#include <string.h> + #include <errno.h> + + #ifdef WIN32 +--- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c ++++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c +@@ -43,7 +43,7 @@ + + #include <limits.h> + #include <math.h> +- ++#include <string.h> + + static AjPRegexp featoutRegUfoFmt = NULL; + static AjPRegexp featoutRegUfoFile = NULL; +--- EMBOSS-6.6.0/ajax/core/ajpdbio.c ++++ EMBOSS-6.6.0/ajax/core/ajpdbio.c +@@ -37,7 +37,7 @@ + + #include <limits.h> + #include <math.h> +- ++#include <string.h> + + + +--- EMBOSS-6.6.0/ajax/core/ajreg.c ++++ EMBOSS-6.6.0/ajax/core/ajreg.c +@@ -32,6 +32,7 @@ + #include "ajlib.h" + + #include "ajreg.h" ++#include <string.h> + + + +--- EMBOSS-6.6.0/ajax/core/ajseqtype.c ++++ EMBOSS-6.6.0/ajax/core/ajseqtype.c +@@ -32,7 +32,7 @@ + #include "ajfeat.h" + #include "ajfile.h" + #include "ajreg.h" +- ++#include <string.h> + + + +--- EMBOSS-6.6.0/nucleus/embindex.c ++++ EMBOSS-6.6.0/nucleus/embindex.c +@@ -35,6 +35,7 @@ + #include "ajnam.h" + + #include <errno.h> ++#include <string.h> + + #define BTENTRYFILE ".ent" + #define KWLIMIT 12 +--- EMBOSS-6.6.0/nucleus/embword.c ++++ EMBOSS-6.6.0/nucleus/embword.c +@@ -36,7 +36,7 @@ + #include "ajutil.h" + + #include <math.h> +- ++#include <string.h> + + + diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml new file mode 100644 index 000000000000..9a479025456e --- /dev/null +++ b/sci-biology/emboss/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + EMBOSS is "The European Molecular Biology Open Software Suite". + EMBOSS is a free Open Source software analysis package specially + developed for the needs of the molecular biology (e.g. EMBnet) user + community. The software automatically copes with data in a variety + of formats and even allows transparent retrieval of sequence data + from the web. Also, as extensive libraries are provided with the + package, it is a platform to allow other scientists to develop and + release software in true open source spirit. EMBOSS also integrates + a range of currently available packages and tools for sequence + analysis into a seamless whole. EMBOSS breaks the historical trend + towards commercial software packages. + </longdescription> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest new file mode 100644 index 000000000000..86558b2b80a5 --- /dev/null +++ b/sci-biology/eugene/Manifest @@ -0,0 +1,10 @@ +AUX eugene-3.6-overflow.patch 252 SHA256 cc8795d5f4525a299bc3e17da1e26c1e5fe3ef0c2371c5bf9de36b5037972fc7 SHA512 ed39c8d4aa73ba9e378a025e740c50f1b431fbb4590e3e9204f789081c8b22aef05fb4ce9ac7a0f22015ee03f73392730894a8dea5f6f16cd4533172e46776ce WHIRLPOOL 775e4167b0efa7dfd1539b01c20f4ce268666840d5c2766222deadacfcc21cf6697c177efde0e777c398ad4c888ee3df1b57113b451b1700ca5965b718c8432f +AUX eugene-3.6-plugins.patch 1784 SHA256 0ec9c0d2bf6009e89612c3d95711b211aefc267d3eb6b75bc6279318256bc46d SHA512 300601ee6abe469460ebbe29c45468d516e5e781ad4b0542e9590de38ba6e98e3697c5f6f92f83212a1aa6da5e0650636af279d82241277c0b43fb5472028fcc WHIRLPOOL 695b8efe382014c6e1c9c44bebab3ed417b7ad736fd7db5623911971926bab284e9bdfb2ee5061287c99a93433d060040285765f37e0b283ecd83717adca5359 +AUX eugene-4.1-format-security.patch 609 SHA256 391521469ce4c6df425084d9b2df611efe2721f563b15843f495064ed72d4553 SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362 WHIRLPOOL 5b703b25d049f9f9fb78d543e72cde8130f9f1e116aac26e1c748897fe6558507d22f2ce08fc7c4e65568f5213fe4fc7de111a58043c88ee94586c4aca3f71e0 +AUX eugene-4.1d-Wformat.patch 2719 SHA256 14277b76320aed2551af0557c373431f556b4b39eac8b73365b373a253a6a543 SHA512 b235c11791caea63109009b858cde7ec179166640f009bf58caf33a8502345360efb71208a330572d7f870c468810bb9ab54db3e2af187a0d2baba7e12c6ff96 WHIRLPOOL be016418800bf8410bb637b2827ddec33366607dc4e0a0bdc014b1ab21599dbc0b26b5363c70d3c52d6da0b92d8119444addceeeac6466dbbdfe54137dec845b +AUX eugene-4.1d-fix-c++14.patch 635 SHA256 80a443e3390ea4fcb13d74f7a3085d690d11409c4212ed35ab592116ff0760f4 SHA512 8ff6a8a2ee4b70b14d0fa9984c057307fe5b7d22e8a26969d82fb1ab7ee30a90cb3520ea8d3e16a59f09dfc46a3310cb43c621fabb31a39216209a4c3523e718 WHIRLPOOL b7c847f0bcf3386b585106345401f7742b0cf4de92556fc5ee98273c1f94ff619e2c640336c7d2d05205c797d6a17616e4775d06f7d1d49ef9cfcbc7015ad6a9 +DIST eugene-4.1d.tar.gz 7473965 SHA256 c160e6b4206e6700c866f38fee2c8fd0d69972d51ebc5b4cb7680774a419f4c0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5 WHIRLPOOL 7ab116acd48648673d2cc633bae26908bf8250c5a17b9d5e8719dfd56edcdf716406b80af26a99700d9ec81e625737c57fe16493f670245f21999fef1c6911eb +EBUILD eugene-4.1d.ebuild 893 SHA256 acf012e114990142a903232435a07e36368831cf4f05ff8746398380383ead3b SHA512 9db8db10b469392a9a124f02dcf1272307c6c44b9734d5f101dd13092701a16f64394408200731a63a14d5ff9e2f3ca83b2391b762b312f1a4d163dffa0b0822 WHIRLPOOL 28c67e6fe06406e0b6648ae6334d48c17f19b0a1959a02df38449553762f5543ef08f1a1cff64bd5f4668b5bc09ba4d9ec2f1b7d7d9ef24920d60a17dcfa9eae +MISC ChangeLog 2831 SHA256 d9ac5006d8a7cd57a6b3a727b21556a20438a300f29b0cf10249ef8630cff0f3 SHA512 c7336aec414a57f81cd85c2b92556a0879bcbb9513b443439be282e02ae4073ce3b5dfad61d0265006a640586d8c0edc08ff6af081d2f794702e1d4b0191e177 WHIRLPOOL be4d86801ceb655f5017be4c527f2a992df7473b257b9febbec8809c1c918beef7844b70dca9c86e2cb0cfb8eb3c38d22b893989d2f4e55da570f0cbd3737e18 +MISC ChangeLog-2015 2009 SHA256 9cc7672d01f3ea069e1465072396b59e81cd8aff667ccf3e5c06776e0bbc571b SHA512 4c25d7d81ca0f63765b8635bff0043d9736e6cec7bc0ed5a4481309851e69bb7a059348e7d5b9a3b0073d68b5e04c3890349a9d0ba92d56f1c319500c58802c6 WHIRLPOOL 664c9da77c8e2bc49b29633d4f04cd9a2e1f1ed7e8f62c276cbe9865c7918ad6903e9cc78b87ac8788e56e331fc08eba18cbf864c0efcf8a72721460d1a82b32 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild new file mode 100644 index 000000000000..dbf8139e9e20 --- /dev/null +++ b/sci-biology/eugene/eugene-4.1d.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Prokaryotic and Eukaryotic gene predictor" +HOMEPAGE="http://eugene.toulouse.inra.fr/" +SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND=" + media-libs/gd[png] + media-libs/libpng:0= + " +RDEPEND="${DEPEND}" + +RESTRICT="test" + +PATCHES=( + # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170 + "${FILESDIR}"/${PN}-3.6-overflow.patch + "${FILESDIR}"/${PN}-3.6-plugins.patch + "${FILESDIR}"/${PN}-4.1-format-security.patch + "${FILESDIR}"/${PN}-4.1d-fix-c++14.patch + "${FILESDIR}"/${PN}-4.1d-Wformat.patch +) + +src_prepare() { + default + sed \ + -e '/SUBDIRS/ s/doc//' \ + -e '/INSTALL.*doc/ s/\(.*\)//' \ + -i Makefile.am || die + eautoreconf +} diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch new file mode 100644 index 000000000000..7222530ad771 --- /dev/null +++ b/sci-biology/eugene/files/eugene-3.6-overflow.patch @@ -0,0 +1,13 @@ +http://bugs.gentoo.org/show_bug.cgi?id=336607 + +--- eugene-3.6/src/Sensor.cc ++++ eugene-3.6/src/Sensor.cc +@@ -224,7 +224,7 @@ + //-------------------------- + void Signals :: PrintS () + { +- char t[7]; ++ char t[10]; + char s = '+'; + + switch (type) { diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch new file mode 100644 index 000000000000..1e910a13d5b1 --- /dev/null +++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch @@ -0,0 +1,43 @@ +http://bugs.gentoo.org/show_bug.cgi?id=297536 + +--- eugene-3.6/src/Makefile.am ++++ eugene-3.6/src/Makefile.am +@@ -20,7 +20,7 @@ + + SUBDIRS = Parametrization GDIF . SensorPlugins + +-AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" ++AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\" + AM_CFLAGS = + + bin_PROGRAMS = eugene +--- eugene-3.6/src/MSensor.cc ++++ eugene-3.6/src/MSensor.cc +@@ -97,7 +97,7 @@ + std::string use_name; + + if (!IsInitialized) { +- PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/"; ++ PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/"; + + // On récupère les couples nom de sensor/priorité du .par + PAR.ResetIter(); +--- eugene-3.6/Makefile.am ++++ eugene-3.6/Makefile.am +@@ -125,7 +125,7 @@ + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images +- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM +@@ -144,6 +144,6 @@ + $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images + $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg +- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval + $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch new file mode 100644 index 000000000000..e6e4a6cc8bd7 --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1-format-security.patch @@ -0,0 +1,16 @@ + src/Hits.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/Hits.cc b/src/Hits.cc +index edfe178..b228be6 100755 +--- a/src/Hits.cc ++++ b/src/Hits.cc +@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int + while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin, + &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8) + { +- if (HSP) fprintf(stderr,HSP); ++ if (HSP) fprintf(stderr, "%s", HSP); + if (phase < 0 && deb > fin) + { + int tmp = deb; diff --git a/sci-biology/eugene/files/eugene-4.1d-Wformat.patch b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch new file mode 100644 index 000000000000..ab6d2bd1d2ee --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch @@ -0,0 +1,84 @@ +Fix -Wformat warnings caused by wrong printf specifiers: +* Sensor.Riken.cc:95:61: warning: format ‘%d’ expects argument of type ‘int’, but +* argument 3 has type ‘std::vector<RAFLgene>::size_type {aka long unsigned int}’ [-Wformat=] +* fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size()); + +--- a/src/Hits.cc ++++ b/src/Hits.cc +@@ -163,7 +163,7 @@ + if (ThisHit != NULL) + for (int i=0; i<*NumHits-1; i++) ThisHit = ThisHit->Next; + +- while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin, ++ while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %ss\n", &deb, &fin, + &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8) + { + if (HSP) fprintf(stderr, "%s", HSP); +--- a/src/SensorPlugins/Est/Sensor.Est.cc ++++ b/src/SensorPlugins/Est/Sensor.Est.cc +@@ -1353,13 +1353,13 @@ + exit(2); + } + +- fprintf(fp, "vPos %d\n", vPos.size()); ++ fprintf(fp, "vPos %zu\n", vPos.size()); + for (int i=0; i< vPos.size();i++ ) + { + fprintf(fp, "vPos %d\t%d\n",i, vPos[i]); + } + +- fprintf(fp, "vESTMatch %d\n", vESTMatch.size()); ++ fprintf(fp, "vESTMatch %zu\n", vESTMatch.size()); + for (int i=0; i< vESTMatch.size();i++ ) + { + fprintf(fp, "vESTMatch %d\t\n", vESTMatch[i]); +--- a/src/SensorPlugins/Riken/Sensor.Riken.cc ++++ b/src/SensorPlugins/Riken/Sensor.Riken.cc +@@ -92,7 +92,7 @@ + + + +- fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size()); ++ fprintf(stderr, "%zu RAFL EST pairs read, ", RAFLtmp.size()); + + sort(RAFLtmp.begin(), RAFLtmp.end(), Before); + +@@ -148,7 +148,7 @@ + } + } + +- fprintf(stderr,"resulting %d\n",RAFL.size()); ++ fprintf(stderr,"resulting %zu\n",RAFL.size()); + fflush(stderr); + + // for (RAFLtmpindice=0; RAFLtmpindice< (int)RAFL.size(); RAFLtmpindice++) { +--- a/src/SensorPlugins/SMachine/Sensor.SMachine.cc ++++ b/src/SensorPlugins/SMachine/Sensor.SMachine.cc +@@ -197,7 +197,7 @@ + fclose(fp); + + if (end ==2) { +- fprintf(stderr, "Error in SpliceMachine splice site file %s, line %d\n", name, len); ++ fprintf(stderr, "Error in SpliceMachine splice site file %s, line %zu\n", name, len); + exit(2); + } + } +--- a/src/SoTerms.cc ++++ b/src/SoTerms.cc +@@ -67,14 +67,14 @@ + j++; + if (line[0] == 'i' && line[1] == 'd') + { +- i = sscanf(line, "id: %s", &value); ++ i = sscanf(line, "id: %s", value); + if (i > 0) + { + char soId[60]; + char soName[60]; + strcpy (soId, value ); + fgets (line, MAX_LINE, fp); +- i = sscanf(line, "name: %s", &value); ++ i = sscanf(line, "name: %s", value); + strcpy (soName, value ); + idToName_[to_string(soId)]=to_string(soName); + nameToId_[to_string(soName)]=to_string(soId); diff --git a/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch new file mode 100644 index 000000000000..a27261c68c06 --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch @@ -0,0 +1,17 @@ +Fix building with C++14, which errors out due to collisions with isinf +from cmath. We don't need to fix ancient broken OSX toolchains. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594700 + +--- a/src/SensorPlugins/Tester/Sensor.Tester.cc ++++ b/src/SensorPlugins/Tester/Sensor.Tester.cc +@@ -18,9 +18,7 @@ + // ------------------------------------------------------------------ + + // MacOS-X kludge. cmath undefines these macros. Turn them into inlines +-#include <math.h> +-inline int (isinf)(double r) { return isinf(r); } +-inline int (isnan)(double r) { return isnan(r); } ++#include <cmath> + + #include <iomanip> + #include <fstream> diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/eugene/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest new file mode 100644 index 000000000000..90a0b4fd4154 --- /dev/null +++ b/sci-biology/exonerate/Manifest @@ -0,0 +1,6 @@ +AUX exonerate-2.2.0-asneeded.patch 362 SHA256 6c3d42a87646760cfede57c38227d379c24a7a1cc867a619667e187680757a98 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0 WHIRLPOOL f136a885fe1d50ec182d855f05a832a25451212bf4047761f76bba4435d9d3b5a47edea4bb77e9f8e082c0adac4e90d1b8537a704622e30fee285b795cd3195b +DIST exonerate-2.2.0.tar.gz 509870 SHA256 0ea2720b1388fa329f889522f43029b416ae311f57b229129a65e779616fe5ff SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c WHIRLPOOL dd7ba7a94b93f41d5ddbc66cc14740973dde20e875f37814229614c85312dcc1de031faab5153bc28be3284144d0f8451bd5e5115f8d9e312e4f88d771ce620c +EBUILD exonerate-2.2.0-r2.ebuild 943 SHA256 df65037ba33c38db84e5efc46e4d4a0750aaf7ac054a378abe3d81c557ae83c7 SHA512 830ed336dd8bb4cf59fb59099d968459530fe37ae8b1874d535dadf4d3874410592d28049abbc8dd0e66ccc4e277cd7855602dcc42e7ac61394249557cf033a2 WHIRLPOOL 192f197662a28d4f56662e402a26231dd951cfe0e8172acf16686f4d2620622d239a7ff128175feb38b91bf8b49aad9f19fe7ed7a533e5bf169eaa68afb6a577 +MISC ChangeLog 2604 SHA256 837c48a04a9024668892f9dd3aa47dba377890e2ecee18a723eb0f8e3b3ca96b SHA512 2d3709081b376cd1abf2af386c2db9cb532ec1442cc5689e3c469124cb7eda7f828ba89ff22f78374581f13c52fa54518597d13367fcb977b63e91d36cd50070 WHIRLPOOL 93af106a3ff2efaa175044e78e6c0cf51d6ea52f05ad87e489f32723493956a5965e0b9a5380c2c5a9c8548e485df4b329500234fe7a1bb58b636250595b7c06 +MISC ChangeLog-2015 1396 SHA256 0f68c730203bf609473c6b2cbdf22db5657b4ebdf9c6627687db5d10d1251518 SHA512 3615e0ddbd40eea5b23937598a96c6e3affe1f28eedd4ecda6d7d4edb195819fac2fb2f84ea9c2736c7d4c07a17e9303ccd918de5b4f228bb1b03ff497c88469 WHIRLPOOL f00b2d484b5b9d5aa440eef62f95a80490e5c8c07b1cec72bda480a2515d4b3338babe2b6a323a249905d0559e23ade6880921a598f568380f83b238872afb70 +MISC metadata.xml 449 SHA256 367ce7f367d26df031c20e887300e862f50ad5bbfe0019f6dd9178267d0408f4 SHA512 ad7dce91503151adedc204bcf1b678ad8bf9bd6a0cc7a207c9225781eeb32e24906794028aba1770260a52e2a6e9c823f138a003153f3e4c49c47228bc112f49 WHIRLPOOL 873ab156b88cf810abd917a9a7e1389fcdaa98f747fc66efa038925b7431233b4255bb877ceb68d62ea84c849358132b87a464546ecdac143476dca474857cef diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild new file mode 100644 index 000000000000..dcd09feac3d9 --- /dev/null +++ b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="Generic tool for pairwise sequence comparison" +HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" +SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" +IUSE="test threads utils" +REQUIRED_USE="test? ( utils )" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) + +src_prepare() { + default + sed \ + -e 's: -O3 -finline-functions::g' \ + -i configure.in || die + mv configure.{in,ac} || die + + eautoreconf +} + +src_configure() { + tc-export CC + + econf \ + --enable-glib2 \ + --enable-largefile \ + $(use_enable utils utilities) \ + $(use_enable threads pthreads) +} + +src_install() { + default + + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch new file mode 100644 index 000000000000..5c428979a1af --- /dev/null +++ b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch @@ -0,0 +1,15 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- a/configure.in ++++ b/configure.in +@@ -289,7 +289,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml new file mode 100644 index 000000000000..09b6a9e09e43 --- /dev/null +++ b/sci-biology/exonerate/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription lang="en"> + exonerate is a generic tool for pairwise sequence comparison + </longdescription> + <use> + <flag name="utils">Install all utilities</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest new file mode 100644 index 000000000000..6bd37964dc72 --- /dev/null +++ b/sci-biology/express/Manifest @@ -0,0 +1,9 @@ +AUX express-1.5.1-buildsystem.patch 1956 SHA256 e4266c79b6d2c34e518cc57a9542543109bcc484511711492b146a7a49cb1187 SHA512 246788b75a7f40c825cc7bf811de2bd44607b7ccf139d7302480ed7faae441ec95d5a37aec7f04effb1e3e47ed774b08291321cd227b0fa79306969b39e93d54 WHIRLPOOL 195d13b46b3e9b3b651c3994148049f7c626dca395c2dbf1ca2eb5e8febb1b8d3d8ef501cd01a62fdc4a5a7a1236970fe6f644f9d5791d3b7fbbe28d7b58a7a3 +AUX express-1.5.1-gcc6.patch 722 SHA256 64be04111783bc1a38089d9a1b901f67c7499b894c51eb2e68b36b061fc0cfae SHA512 bbc7d7980bc88e241a76ad2b8a661ac8232f2cbc1a8cbf526b43905f9cdc52b57aadf8fb6bb03181b51893ac4e9d384ababb6d34582f7e24e6ef2ecc8fbfd73f WHIRLPOOL 9fa75d753b6432fb5e6bdb52ea54ba4d5fcf57fbade90ca2bb93c291c0807fc597d0844f7b6821822cd5b22d18060e3654d9b86ad9c5f1f544bcf9e9e4cbfedf +DIST express-0.9.5-src.tgz 766024 SHA256 e17250d62750560c2dc9cb579f58784b5076afb74088f36523ddd623e08bc022 SHA512 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+inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +CMAKE_USE_DIR="${S}/src" + +src_prepare() { + sed \ + -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \ + -e '1 a find_package(Boost 1.52 COMPONENTS filesystem program_options system thread)' \ + -e '1 a find_package(ZLIB)' \ + -e '/add_executable/ a include_directories("/usr/include/bamtools")' \ + -i src/CMakeLists.txt || die + + cmake-utils_src_prepare +} diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild new file mode 100644 index 000000000000..62e5361f529f --- /dev/null +++ b/sci-biology/express/express-1.5.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + dev-libs/protobuf + dev-util/google-perftools + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch + "${FILESDIR}"/${P}-gcc6.patch +) + +src_configure() { + local mycmakeargs=( + -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools" + ) + cmake-utils_src_configure +} diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch new file mode 100644 index 000000000000..fca5feadd111 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-buildsystem.patch @@ -0,0 +1,55 @@ + CMakeLists.txt | 8 +++----- + src/CMakeLists.txt | 4 ++-- + 2 files changed, 5 insertions(+), 7 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index c768e28..65d5633 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1) + set(${PROJECT_NAME}_VERSION_MINOR 5) + set(${PROJECT_NAME}_VERSION_PATCH 1) + +-set(CMAKE_CXX_FLAGS "-Wall") +- + set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}") + + set(CMAKE_BUILD_TYPE Release) +-set(Boost_USE_STATIC_LIBS ON) ++set(Boost_USE_STATIC_LIBS OFF) + + find_package(Boost 1.39 + COMPONENTS +@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB) + + find_package(Protobuf) + if (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 1) + else (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 0) + endif(PROTOBUF_FOUND) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 1cc0c01..8929d1f 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC) + if(WIN32) + set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") + else(WIN32) +- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") ++ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread") + endif(WIN32) + + if (PROTOBUF_FOUND) +- set(LIBRARIES ${LIBRARIES} "libprotobuf.a") ++ set(LIBRARIES ${LIBRARIES} "protobuf") + endif(PROTOBUF_FOUND) + + target_link_libraries(express ${LIBRARIES}) diff --git a/sci-biology/express/files/express-1.5.1-gcc6.patch b/sci-biology/express/files/express-1.5.1-gcc6.patch new file mode 100644 index 000000000000..8a608b97b056 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-gcc6.patch @@ -0,0 +1,19 @@ +Bug: https://bugs.gentoo.org/610692 + +--- a/src/targets.cpp ++++ b/src/targets.cpp +@@ -113,12 +113,12 @@ + + double ll = LOG_1; + double tot_mass = mass(with_pseudo); +- double tot_eff_len = cached_effective_length(lib.bias_table); ++ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table)); + if (neighbors) { + foreach (const Target* neighbor, *neighbors) { + tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo)); + tot_eff_len = log_add(tot_eff_len, +- neighbor->cached_effective_length(lib.bias_table)); ++ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table))); + } + } + ll += tot_mass - tot_eff_len; diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/express/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest new file mode 100644 index 000000000000..936de1abe1eb --- /dev/null +++ b/sci-biology/fasta/Manifest @@ -0,0 +1,9 @@ +AUX 35.4.10-ldflags.patch 1036 SHA256 21b6c290ca565c50376da61cd980f21f7a96598ea5da046294321d8d6be5d5fe SHA512 8136536c7f9887920a045dbcd04fa9d01dc0a3b22ed0a1771df715e288d6c889d87b0a6d0f52c947b54185f6a5e92fe902316b502074200a13820cac9dfa6594 WHIRLPOOL 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91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild new file mode 100644 index 000000000000..8cad4d2a8b08 --- /dev/null +++ b/sci-biology/fasta/fasta-35.4.10.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="2" + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" +SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="debug cpu_flags_x86_sse2 test" + +DEPEND="test? ( app-shells/tcsh )" +RDEPEND="" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ $(tc-getCC) == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT=$(tc-getCC) + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + epatch "${FILESDIR}"/${PV}-ldflags.patch +} + +src_compile() { + cd src + emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die +} + +src_install() { + dobin bin/* || die + doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die + dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die +} diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild new file mode 100644 index 000000000000..96494b79aa34 --- /dev/null +++ b/sci-biology/fasta/fasta-36.3.5e.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" +SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="debug cpu_flags_x86_sse2 test" + +DEPEND="test? ( app-shells/tcsh )" +RDEPEND="" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ $(tc-getCC) == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT=$(tc-getCC) + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + epatch "${FILESDIR}"/${P}-ldflags.patch + + sed \ + -e 's:-ffast-math::g' \ + -i make/Makefile* || die + +} + +src_compile() { + cd src || die + emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all +} + +src_test() { + cd test || die + FASTLIBS="../conf" bash test.sh || die +} + +src_install() { + local bin + dobin bin/* + + pushd bin > /dev/null || die + for bin in *36; do + dosym ${bin} /usr/bin/${bin%36} || die + done + popd + + insinto /usr/share/${PN} + doins -r conf/* data seq + + doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} + dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} +} diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch new file mode 100644 index 000000000000..c3b7a9b56904 --- /dev/null +++ b/sci-biology/fasta/files/35.4.10-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/make/Makefile.pcom b/make/Makefile.pcom +index a808667..405be95 100644 +--- a/make/Makefile.pcom ++++ b/make/Makefile.pcom +@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm + + res_stats : res_stats.o scale_se.o +- $(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch new file mode 100644 index 000000000000..a6eeabfdf46c --- /dev/null +++ b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch @@ -0,0 +1,74 @@ + make/Makefile.pcom | 8 ++++---- + make/Makefile.pcom_s | 8 ++++---- + make/Makefile.pcom_t | 8 ++++---- + 3 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/make/Makefile.pcom b/make/Makefile.pcom +index 9c5f801..33fc001 100644 +--- a/make/Makefile.pcom ++++ b/make/Makefile.pcom +@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm +diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s +index dc53001..8a45044 100644 +--- a/make/Makefile.pcom_s ++++ b/make/Makefile.pcom_s +@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm +diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t +index 8a71438..5b08a50 100644 +--- a/make/Makefile.pcom_t ++++ b/make/Makefile.pcom_t +@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/fasta/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest new file mode 100644 index 000000000000..fcba17331e2a --- /dev/null +++ b/sci-biology/fasttree/Manifest @@ -0,0 +1,14 @@ +AUX CMakeLists.txt 948 SHA256 60c21f04ea3ef04782dfc0328e317b6d04197a45af4d15c5c43f4f87a1f82c44 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3 WHIRLPOOL edc50a85eaec6161924f38569c33ccd35170f9ac89e17741e4a87ceb350b165fdf6e118c20bfd27a02ec1e01aa76be8665908f39c531a292d3d1b706e6c1b25a +AUX fasttree-2.1.7-format-security.patch 783 SHA256 83e4b1b6de9fb5f8875a4d53ed274866bb34bbb36610b0f7bbda22ebea60fd07 SHA512 cabda061de75a1e1b34732946448ee08717f265d7fa8ea413f56eb8bad150ebde9f376a13591167a7786caf17a0d4bb1f8cb7176b74965a47f79b9608d32bcf8 WHIRLPOOL cec0331b56114bd36085c1a64b048979579984b769102358365e4c719b03b1fb6b52919f4397b97c424613811e4e1ef572f3e6fb595aa5340e25d6881bc46e97 +AUX fasttree-2.1.8-format-security.patch 783 SHA256 cd838048ce9b99adb462f75cdb56ec65274e0c96340685c736858580b38c2579 SHA512 9bbf66cddca2b6c202fdeeab4092036852cb1ebe132ebf4d96cba1bea75bb5668dd6ee97d4d020a4b7cf7111bee6d0c3004b0bd74ee4685ef98eeeb5e9a23eb3 WHIRLPOOL d20139d2ba391ed11924b70495d16fdf706171953f712214b5d0a83395cd97a0395c7dc8a6e586c3ee87579c1124c7599cc89e933ba684940909daa7eda11f2d +DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775 +DIST FastTree-2.1.8.c 385231 SHA256 b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 SHA512 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000000000000..aa5979522691 --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +SRC_URI=" + http://www.microbesonline.org/fasttree/FastTree-${PV}.c + http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c + http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="double-precision openmp cpu_flags_x86_sse3" + +REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) + +src_unpack() { + mkdir "${S}" || die + cd "${S}" || die + unpack ${A} + cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die +} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) + $(cmake-utils_use_use openmp) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild new file mode 100644 index 000000000000..7df71ee4474d --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +SRC_URI=" + http://www.microbesonline.org/fasttree/FastTree-${PV}.c + http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c + http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="double-precision openmp cpu_flags_x86_sse3" + +REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) + +src_unpack() { + mkdir "${S}" || die + cd "${S}" || die + unpack ${A} + cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die +} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) + $(cmake-utils_use_use openmp) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt new file mode 100644 index 000000000000..e7c53afdaf36 --- /dev/null +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required (VERSION 2.6) +project(fasttree C) + +option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) +option(USE_DOUBLE "Use double precission" OFF) +option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) + +if(USE_OPENMP) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif(USE_OPENMP) + +if(USE_DOUBLE) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif(USE_DOUBLE) + +if(NOT HAS_SSE3) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif(NOT HAS_SSE3) + + +add_executable(FastTree FastTree-${VERSION}.c) +add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) + +target_link_libraries(FastTree m) +target_link_libraries(FastTreeUPGMA m) + +install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) + +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch new file mode 100644 index 000000000000..31dafdad46de --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.7.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.7.c ++++ b/FastTreeUPGMA-2.1.7.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch new file mode 100644 index 000000000000..15f5c174ec40 --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.8.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.8.c ++++ b/FastTreeUPGMA-2.1.8.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml new file mode 100644 index 000000000000..802ef76f0cb9 --- /dev/null +++ b/sci-biology/fasttree/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="double-precision"> + use double precision instead of single-precision floating point + (2x memroy required) + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest new file mode 100644 index 000000000000..1ef2125ee6a5 --- /dev/null +++ b/sci-biology/finchtv/Manifest @@ -0,0 +1,6 @@ +DIST finchtv_1_3_1.tar.gz 6706911 SHA256 03fccbf1ab09b571bbf55d0b71dd86975513b7a6c8d54795055a184b4eda8858 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8 WHIRLPOOL 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SampleData +} diff --git a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild new file mode 100644 index 000000000000..09ab304a7a3d --- /dev/null +++ b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +MY_PV="${PV//./_}" +MY_P=${PN}_${MY_PV} + +DESCRIPTION="Graphical viewer for chromatogram files" +HOMEPAGE="http://www.geospiza.com/finchtv/" +SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" + +LICENSE="finchtv" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MY_P}" + +QA_PREBUILT="opt/bin/*" + +src_install() { + exeinto /opt/bin + doexe finchtv + + dodoc ReleaseNotes.txt + docinto html + dodoc -r Help/* + + insinto /usr/share/doc/${PN} + doins -r SampleData + + newicon Help/media/FinchTV_Mac_App.png ${PN}.png +} diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml new file mode 100644 index 000000000000..a46ebf47e871 --- /dev/null +++ b/sci-biology/finchtv/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription lang="en"> +A cross-platform graphical viewer for chromatogram files. +</longdescription> +</pkgmetadata> diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest new file mode 100644 index 000000000000..b6e219b93684 --- /dev/null +++ b/sci-biology/foldingathome/Manifest @@ -0,0 +1,7 @@ +AUX 7.3/folding-conf.d 339 SHA256 016af8d64434d3a13d336055347dcae8e486dedbcfe66d288c3b961e662175a0 SHA512 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/opt/foldingathome/config.xml +# Run /opt/foldingathome/initfolding to reconfigure that. +# +# The options that may be passed to the Folding client can be obtained +# by running /opt/foldingathome/FAHClient --help +# +FOLD_OPTS="" +PIDFILE=/run/folding diff --git a/sci-biology/foldingathome/foldingathome-7.4.4-r2.ebuild b/sci-biology/foldingathome/foldingathome-7.4.4-r2.ebuild new file mode 100644 index 000000000000..92d3b277ea7a --- /dev/null +++ b/sci-biology/foldingathome/foldingathome-7.4.4-r2.ebuild @@ -0,0 +1,126 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit versionator user systemd + +MY_BASEURI="https://fah.stanford.edu/file-releases/public/release/fahclient" +MY_64B_URI="${MY_BASEURI}/centos-5.3-64bit/v$(get_version_component_range 1-2)/fahclient_${PV}-64bit-release.tar.bz2" +MY_32B_URI="${MY_BASEURI}/centos-5.5-32bit/v$(get_version_component_range 1-2)/fahclient_${PV}-32bit-release.tar.bz2" + +DESCRIPTION="Folding@Home is a distributed computing project for protein folding" +HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html" +SRC_URI="x86? ( ${MY_32B_URI} ) + amd64? ( ${MY_64B_URI} )" + +RESTRICT="mirror bindist strip" + +LICENSE="FAH-EULA-2014 FAH-special-permission" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Expressly listing all deps, as this is a binpkg and it is doubtful whether +# i.e. uclibc or clang can provide what is necessary at runtime +RDEPEND="app-arch/bzip2 + sys-devel/gcc + sys-libs/glibc + sys-libs/zlib" + +S="${WORKDIR}" + +QA_PREBUILT="opt/foldingathome/*" + +pkg_setup() { + elog "" + elog "Special permission is hereby granted to the Gentoo project to provide an" + elog "automated installer package which downloads and installs the Folding@home client" + elog "software. Permission is also granted for future Gentoo installer packages on the" + elog "condition that they continue to adhere to all of the terms of the accompanying" + elog "Folding@home license agreements and display this notice." + elog "-- Vijay S. Pande, Stanford University, 07 May 2013" + elog "" + elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )" + elog "" + + enewuser foldingathome -1 -1 "${EPREFIX}"/opt/foldingathome +} + +src_install() { + local myS="fahclient_${PV}-64bit-release" + use x86 && myS="${myS//64bit/32bit}" + exeinto /opt/foldingathome + doexe "${myS}"/{FAHClient,FAHCoreWrapper} + + newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome + cat <<EOF >"${T}"/fah-init +#!/sbin/openrc-run +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\"" +command="${EPREFIX}/opt/foldingathome/FAHClient" +command_args="\${FOLD_OPTS}" +command_user=foldingathome +command_background=1 +pidfile="\${PIDFILE}" +EOF + newinitd "${T}"/fah-init foldingathome + + cat <<EOF >"${T}"/fah-init.service +[Unit] +Description=Folding@Home V7 Client +Documentation=https://folding.stanford.edu/home/the-software/ + +[Service] +Type=simple +User=foldingathome +WorkingDirectory="${EPREFIX}/opt/foldingathome" +PIDFile=/run/fahclient.pid +ExecStart=./FAHClient -v start +ExecReload=./FAHClient -v restart +ExecStop=./FAHClient -v stop +KillMode=process + +[Install] +WantedBy=multi-user.target +EOF + systemd_newunit "${T}"/fah-init.service foldingathome.service + + fowners -R foldingathome:foldingathome /opt/foldingathome +} + +pkg_postinst() { + elog "To run Folding@home in the background at boot:" + elog "(openrc)\trc-update add foldingathome default" + elog "(systemd)\tsystemctl enable foldingathome" + elog "" + if [ ! -e "${EPREFIX}"/opt/foldingathome/config.xml ]; then + elog "No config.xml file found -- please run" + elog "emerge --config ${P} to configure your client, or specify" + elog "all necessary runtime options in FOLD_OPTS within" + elog "${EPREFIX}/etc/conf.d/foldingathome" + elog "" + fi + if [[ -n ${REPLACING_VERSIONS} ]]; then + elog "NOTE, the 'initfolding' helper script has been dropped, please" + elog "use emerge --config ${P} or run FAHClient --configure directly" + elog "and adjust file permissions and ownership yourself" + elog "" + fi + elog "Please see ${EPREFIX}/opt/foldingathome/FAHClient --help for more details." + einfo "" + einfo "The original package maintainer encourages you to acquire a username and join team 36480." + einfo "http://folding.stanford.edu/English/Download#ntoc2" + einfo "" +} + +pkg_postrm() { + elog "Folding@home data files were not removed." + elog "Remove them manually from ${EPREFIX}/opt/foldingathome" +} + +pkg_config() { + cd "${EPREFIX}"/opt/foldingathome || die + su foldingathome -s /bin/sh -c "./FAHClient --configure" +} diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml new file mode 100644 index 000000000000..2a9179e910a9 --- /dev/null +++ b/sci-biology/foldingathome/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> + <email>axs@gentoo.org</email> + <name>Ian Stakenvicius</name> +</maintainer> +<maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> +</maintainer> +</pkgmetadata> diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest new file mode 100644 index 000000000000..0bfa7d0cfa84 --- /dev/null +++ b/sci-biology/gatk/Manifest @@ -0,0 +1,6 @@ +DIST gatk-2.4.tar.gz 9106774 SHA256 db0be90ef5182866a1f936742fba20b317ce582556e19acb69de2a8894f7383a SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace WHIRLPOOL 1fa7a73f317db82c313ea112ffaa6466c2b17384f1ad8d06c74a3f4764dfd822f036cc2dc99890c157fc2c32ce299a4a7d0c73cafc72dd7ad955d75053745b2c +EBUILD gatk-2.4.ebuild 914 SHA256 2520ab79fd82f6f22b5a70ddecf0ca27d368dfae9e8af55e8781ea97d4230af5 SHA512 a1a6fc27407bbc13247e866ed2dbc34428009091bf85e73776b5a47a95f8daca976060ecf092c4a68fee8afc1068f10aebc743e879b837b8ce0cf8ee461f6b6d WHIRLPOOL 53b8219fa5d5845ef4a1ee46e54d0d2bd82377284dd58e3d879b83187f72a2cc97072284ce7c8ad42154aeba1e3367759f966b6a859351dd94e79504dc8c50d5 +EBUILD gatk-9999.ebuild 899 SHA256 3951b5deea9081f8417024f976e30268d469b3636feda97b30957485dff8fb1c SHA512 1bffd684f48d50a84d4c0c55f6ed8ac10bfe7ca93d35ec32d282922ad8f1bdcee5aee284c4202cb547b9a332c3aaf32b4ebf5f4488b83856a9ac11f67f8b36a2 WHIRLPOOL 22c0b9c3c4c2ebcefc6c8be57097be69a93408ddbcea34f4051c5a00367d83bc2b6d366eecf5e3b881ac4dc5da25cfff1ba54ae9c6d6befe7d02e7812f9879d1 +MISC ChangeLog 2986 SHA256 48aba811073c7fd29bc04e07796c430290baa81f5ed6a7ea090cb2ea552df3a3 SHA512 b767dac7a1ce7d97f4e698684f4ec427e2170a9f2296d67b4ef768173377e169536cee95377bac4d2bb8640e23da887044c1bd1f8da02890e955a6a400970755 WHIRLPOOL 6a43a43136ce1e1bced58b6fca10e17ec23a21f7fd6c7c37e20c893ca4610a266f69071a4c1588eff7660adba9006633b52e6c8b38250975c190463866f61c79 +MISC ChangeLog-2015 1270 SHA256 9aab10f16c8e6afe3e4ae601f67c8effd9f1aafa2686c27840afdd359ea91f44 SHA512 02f5130b2615c68a952a5374f0401535e0cb4a8d7aeb8b420a6077caae8b6423dc480f9b88aeabdcd21ffbb9ad6064ad2b4d498827f42fdc83368c4ac848e035 WHIRLPOOL 53b1dab0452dfb0bcc7550ac3e16080ac7d8e647b61b02dc36ae10571404eca4198379ae84b60a3dc528a14b722c52b0159d8ea2e0770d32167fc2e53fa3deed +MISC metadata.xml 349 SHA256 4a02ed79b669b9458e55ad200851ea6b35f5af76b3a867df5fa3661e265eceb3 SHA512 1605fb041826c7197edcd3658343ed3ac50aea7dfa53262700b9f9e1a45ee81df501e55bf1e8417201f0f2709b6b6e29bb6e5036b7c187846b4dec5e89903f54 WHIRLPOOL 2ffd8a0b69eb6d47aae4b65e5f23f4b7149f518b3e268743f44ae2034fd526aa82530369a2503fcd29819d19a729dcaec7e6ac9ea3f8387593b37ef7feb4fafd diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild new file mode 100644 index 000000000000..1a885b922b87 --- /dev/null +++ b/sci-biology/gatk/gatk-2.4.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +EANT_BUILD_TARGET="dist" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" + +inherit java-pkg-2 java-ant-2 vcs-snapshot + +DESCRIPTION="The Genome Analysis Toolkit" +HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit" +SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64" + +COMMON_DEPS="" +DEPEND=" + >=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=" + >=virtual/jre-1.6 + ${COMMON_DEPS}" + +src_prepare() { + sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar dist/*.jar + java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar + java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar +} diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild new file mode 100644 index 000000000000..fee2670ad219 --- /dev/null +++ b/sci-biology/gatk/gatk-9999.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +EANT_BUILD_TARGET="dist" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" + +inherit git-2 java-pkg-2 java-ant-2 + +DESCRIPTION="The Genome Analysis Toolkit" +HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit" +SRC_URI="" +EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="" + +COMMON_DEPS="" +DEPEND=" + >=virtual/jdk-1.6 + dev-vcs/git + ${COMMON_DEPS}" +RDEPEND=" + >=virtual/jre-1.6 + ${COMMON_DEPS}" + +src_prepare() { + sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar dist/*.jar + java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar + java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar +} diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml new file mode 100644 index 000000000000..8c1bb65774cc --- /dev/null +++ b/sci-biology/gatk/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">broadgsa/gatk</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest new file mode 100644 index 000000000000..a059491bd198 --- /dev/null +++ b/sci-biology/gibbs/Manifest @@ -0,0 +1,5 @@ +DIST gibbs-3.1.tar.gz 563300 SHA256 e8bd62b7d2580b00fc0cdf32ed75ac1ffac29747c75227269a75fd587ba77b69 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52 WHIRLPOOL 9d8dd711d54a03163facbff197db7fd5406a4c4a47c542e3428113945e0bdf6b45f0a48296dde9ddcb32e7de6ae2794e8a81151bb0d21ca34be14c7b6bf4ce21 +EBUILD gibbs-3.1.ebuild 1080 SHA256 f9fa066bf6ec09205f6577af5f187bd545606c4f0b3866f1a898a604c33e9c5f SHA512 d07fc647931b6d8c0634a4d089429fade0f3d3262e0369236420963ba7dd6e3450a66cc0d4fe3ecc884a67e6aba8322d3492fc7a8b7a9fa8b32813e3973bc1fb WHIRLPOOL b605f4d794323c9ab2bb09fbbdb1155198aafb1109c640b463f7e23ad4d6ac82428624e22e84abe75fe414969d07f3c6b1687a7da48b831fbd0209f90b3b2734 +MISC ChangeLog 2439 SHA256 a7e03ccdd598edff2c7eb257b11e4e6d9da006e33beed548b71772709bf13580 SHA512 30db60a8820d0f8c4886a74b81f25a5bf6dfc9a90a11336ffb2041aaa3e38e4f7a31cd24e84ff6161a561a105ea80c0512264750c1b90fa4c364860b2bd66480 WHIRLPOOL 080badadd8d472173308c72729e606dbe4daac5db4946a1db3e5f8e90ca88ef0c1f238d9e3f7c6f00515c69c05ca24300c4899971cb45654594cd53e848e66d9 +MISC ChangeLog-2015 1749 SHA256 b3dd3175ff64335c168eeedbd56c9442d9cdb4fadc70d41b02593e432a0899fb SHA512 1ed351dbdb14799f4de91000557550a3131491a8e256f71c338cfd3fdcdea5afa06791a67497285363b50eedff64d4516bf439209e3b4cca3920d2e4f95b9540 WHIRLPOOL b9c5d56102b24599f983f4955c36a376b0770251935f7839ee72d08b650f71e3dfbde3c8662f546e7d5a3c1913c11ae30b790c030f2e4a393a4831e5ba9a46c3 +MISC metadata.xml 483 SHA256 365570f5052119268076375e196e23917708f6dfd4108420b6691e80a3642953 SHA512 3f86f0f0f673f78c65187f282c0346fccab1102a01869811afd73a6070a3efa032ff9d427a57a9e8a9922cdc055a33d6bccb771eda1196d6667b3076035fd077 WHIRLPOOL 1472e67be1e31b00d9be39c59f6b8c9f1a6eadeef9d9c7f1e56e94dce60ac3dc5fab021e1fde5e0dc35f193495985df24fc191f018f49dcadcffd6de87c2f3b6 diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild new file mode 100644 index 000000000000..de8322a5068e --- /dev/null +++ b/sci-biology/gibbs/gibbs-3.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils multilib + +DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences" +HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html" +SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="mpi" +KEYWORDS="amd64 x86" + +DEPEND=" + mpi? ( + virtual/mpi + sys-cluster/mpe2 )" +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \ + -e 's/-Werror//' \ + -i configure.in || die + autotools-utils_src_prepare +} + +src_configure() { + if use mpi; then export CC=mpicc; fi + local myeconfargs=( $(use_enable mpi) ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + exeinto /usr/$(get_libdir)/${PN} + doexe *.pl + dodoc README ChangeLog +} + +pkg_postinst() { + einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}." + einfo "These scripts require installation of sci-biology/bioperl." +} diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml new file mode 100644 index 000000000000..fc9e1d2b4594 --- /dev/null +++ b/sci-biology/gibbs/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + The Gibbs motif sampler stochastically examines candidate alignments + in an effort to find the best alignment as measured by the maximum + a posteriori (MAP) log-likelihood ratio. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest new file mode 100644 index 000000000000..3d68f9533801 --- /dev/null +++ b/sci-biology/glimmer/Manifest @@ -0,0 +1,13 @@ +AUX glimmer-3.02-glibc210.patch 799 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b SHA512 7a6b05a9b626dbefdabf4535026077b6259747cd2603847e6aa7fed991d456d87bc658ca923959fbdd2ceb4e43e096d46925946ffc135277794a1a6399433a1b WHIRLPOOL 797232ac343731e37800495a50bbdb4c254d04c52ec9ad5b3e57b2ad623bb93c4024fe150f7d8bc2dc4f0d0a83cd75d511d985a62bf4a02bcb04ec813528c606 +AUX glimmer-3.02-jobserver-fix.patch 433 SHA256 19f45973fa230874274d779b03aba73abbecf1344d4a0d795d70256a82036e15 SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d WHIRLPOOL a93193e48512a0cd8c6996d77ee8f1fd91b18cf00e6c99ec6c59dc9953bcb5ee5a90180b317ffb99337666e451da91f77f14a805f43026c1819ec596bb1268c1 +AUX glimmer-3.02-ldflags.patch 2057 SHA256 95d391acdbf6d84440c2f3d96791e9f97776b7a248c9546738cc9df88711a28e SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8 WHIRLPOOL d68752a5c3f78195bfabd116d19ca22ba90af7b817bfa29b9e0cc5614391e32cc3dd8cdd72e3ab642f4b52c48305ed8c7ab32ed622826b720b6228617ed682fe +AUX glimmer-3.02b-jobserver-fix.patch 433 SHA256 19f45973fa230874274d779b03aba73abbecf1344d4a0d795d70256a82036e15 SHA512 51bb9c5223a034b4d5d76df33528172d8f642d8fac0d51a1c4ad1be74c253a4859ed87ccad219bf5cdbcd1b5d4684061ebd91751c7b213767e1c950af13a430d WHIRLPOOL a93193e48512a0cd8c6996d77ee8f1fd91b18cf00e6c99ec6c59dc9953bcb5ee5a90180b317ffb99337666e451da91f77f14a805f43026c1819ec596bb1268c1 +AUX glimmer-3.02b-ldflags.patch 2057 SHA256 95d391acdbf6d84440c2f3d96791e9f97776b7a248c9546738cc9df88711a28e SHA512 aeeac4ee64e358c932a91c4b660c83f8afbfb3ef1b292c9cf8598c56d8645f0d820f4bbc545319e91fe2e65efa5d3aec22f381f75e12aa1574bb7a3b854df6a8 WHIRLPOOL d68752a5c3f78195bfabd116d19ca22ba90af7b817bfa29b9e0cc5614391e32cc3dd8cdd72e3ab642f4b52c48305ed8c7ab32ed622826b720b6228617ed682fe +AUX glimmer-3.02b-rename_extract.patch 9286 SHA256 275f783f675729e5b39bea26e9a506dd2a1b675ef20f9a611ca50cb94b1ad272 SHA512 b5c08ba7ac973e723aeb8bc8808f69eded90b1e59c9d14804519d1d689e820193bf71860026642b3aed049881289c651f9cfd45bc05d53d73a2e9ab891f9b342 WHIRLPOOL b5cc7d1d3734fc373c2a96d82bbcbb2a531bdc8040a7543d0ffdfcc9f4889ba9c89854ba4f99f9b4c1be30eb7a477530ee707bfadcc4ef180b1d6fcda26e7334 +DIST glimmer302.tar.gz 5637075 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c WHIRLPOOL c3eedb4a3a65043a69d632360608f04382117b8f7f3718eae328a1aa14f9f5d6d9ae6f05e0a83a09af5eb9e6b0c7b0ae26cb820813341aa5d7fa3f6002938ce8 +DIST glimmer302b.tar.gz 5637975 SHA256 ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 WHIRLPOOL bbce6f57546e6cc77801ac7f5e783510feafc2e120a8727e848a95dd9e2d966538e56cb7be597c2a463d9b372c8586a389d639e1377708a27bd56f81b37fea1f +EBUILD glimmer-3.02-r3.ebuild 1354 SHA256 9f2d65a25c543e474a289594985fecf3c6269f3281aaf839092f81d22c20e0ce SHA512 c2930627e031436d36b87ac8ec80f672700faa91db3aba175e428e9190ae8129a66288c08f10e501e4c4de98fb6a9aebdb46c7300c0ad6b17768a6d1e53161ea WHIRLPOOL b70962f6b2012366f2d0f1cc3da1d52311e435221e1e0fc851b9e0af70dc60563785e9373935a956167bd3c5d83b151a13038611d30a0eb40d5c44603568f266 +EBUILD glimmer-3.02b.ebuild 1700 SHA256 bce6feeb5858c7678d8f31968c08e1ccb251d580d81e4d755bbb5cbd4d4af51e SHA512 f66d205a926c198c92a8798cd7cdf20bc9620225fc67a20d097b70e08db995c05c2ebf9e7d760d123e5e9dee8c11b862070547ed1a751508d7b07d86ae983062 WHIRLPOOL c6e8335d7c5d3847f17284d505d4fd3281b57f855c646c1ed6269344588b0cc09e3c1cf07b12082dedb2aa33391960a1a3970b75642c3841f2583ec48d7ed77d +MISC ChangeLog 2727 SHA256 5076134d433536116e5b368869f9a4a5edef27a97d45ad0389e166437045cdd9 SHA512 94f62785b5fb5059a090fdb9c3fc862df6011ed9efd3940d0068169ab9fb84bd882c992c3fe64a4044a9c76b90f6ece699a9078c39589fe3ae9444d7f976a7ff WHIRLPOOL 85fbf73be715d4fdaf2e6278e3e7c3517e2349bae771439298cb5614102a782d94bb20b2b272a31cbbc52d6b0e0282101d0cc0418a1534019c4d1c8766741efe +MISC ChangeLog-2015 2304 SHA256 d33edc8f014290bdadb5508d59dd3a3b9fe115aba78d667bee1312034dc168da SHA512 ed293293a8875e5c31a515e8ee1c1bb1c73774201325280382fbb618cb6c6b86095715c6c126e1aa5de6b6a8bd55709e3a473b5750b4bf8ee081047aa90e2572 WHIRLPOOL fae3fb2318dbdf875c4c507b18d7c0016aa3cfded21f16236804ddb012e14053fb52b4541dad3e744c4336dbec2951e70682897d6b10cc922a80cc82a566dbd9 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch new file mode 100644 index 000000000000..f6051ec82054 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch @@ -0,0 +1,24 @@ +diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc +--- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000 ++++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000 +@@ -443,7 +443,7 @@ + // Return a subscript corresponding to character ch . + + { +- char * p; ++ const char * p; + + p = strchr (CONVERSION_STRING, tolower (ch)); + if (p == NULL) +diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc +--- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000 ++++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000 +@@ -1981,7 +1981,7 @@ + // model) for character ch . + + { +- char * p; ++ const char * p; + + p = strchr (ALPHA_STRING, tolower (Filter (ch))); + if (p == NULL) diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch new file mode 100644 index 000000000000..91498b116d12 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch @@ -0,0 +1,22 @@ +diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile +--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 +@@ -2,12 +2,12 @@ + + + all: +- @ TGT=objs +- @ $(dosubdirs) +- @ TGT=libs +- @ $(dosubdirs) +- @ TGT=progs +- @ $(dosubdirs) ++ @+ TGT=objs ++ @+ $(dosubdirs) ++ @+ TGT=libs ++ @+ $(dosubdirs) ++ @+ TGT=progs ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC = cc +-endif +- +-ifneq "$(origin CPPFLAGS)" "environment" +-CPPFLAGS= +-endif +- +-ifneq "$(origin CFLAGS)" "environment" +-CFLAGS = +-endif +- +-ifneq "$(origin CDEFS)" "environment" +-CDEFS = +-endif +- +-ifneq "$(origin CXX)" "environment" +-CXX = g++ +-endif +- +-ifneq "$(origin CXXFLAGS)" "environment" +-CXXFLAGS= +-endif +- +-ifneq "$(origin CXXDEFS)" "environment" +-CXXDEFS= -D__cplusplus +-endif +- +-ifneq "$(origin AR)" "environment" +-AR = ar +-endif +- +-ifneq "$(origin ARFLAGS)" "environment" +-ARFLAGS = rvs +-endif +- +-ifneq "$(origin LDFLAGS)" "environment" +-LDFLAGS = +-endif ++CC ?= cc ++CXX ?= g++ ++CXXFLAGS ?= ++CXXDEFS = -D__cplusplus ++AR ?= ar ++ARFLAGS ?= rvs + + #### Delete default suffix rules + .SUFFIXES: +@@ -359,13 +326,13 @@ $(PROGS): + cd $(LOCAL_OBJ); \ + if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + else \ + cd $(LOCAL_OBJ); \ + if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + fi ; + +diff --git a/src/c_make.glm b/src/c_make.glm +index 0decc17..b82131c 100644 +--- a/src/c_make.glm ++++ b/src/c_make.glm +@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen + + SUBDIRS = Common ICM Glimmer Util + +-CFLAGS = -g -Wall +-CXXFLAGS = -g -Wall +- +-LDFLAGS = -g -lm ++LIBS = -lm + + + #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch new file mode 100644 index 000000000000..91498b116d12 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch @@ -0,0 +1,22 @@ +diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile +--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 +@@ -2,12 +2,12 @@ + + + all: +- @ TGT=objs +- @ $(dosubdirs) +- @ TGT=libs +- @ $(dosubdirs) +- @ TGT=progs +- @ $(dosubdirs) ++ @+ TGT=objs ++ @+ $(dosubdirs) ++ @+ TGT=libs ++ @+ $(dosubdirs) ++ @+ TGT=progs ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC = cc +-endif +- +-ifneq "$(origin CPPFLAGS)" "environment" +-CPPFLAGS= +-endif +- +-ifneq "$(origin CFLAGS)" "environment" +-CFLAGS = +-endif +- +-ifneq "$(origin CDEFS)" "environment" +-CDEFS = +-endif +- +-ifneq "$(origin CXX)" "environment" +-CXX = g++ +-endif +- +-ifneq "$(origin CXXFLAGS)" "environment" +-CXXFLAGS= +-endif +- +-ifneq "$(origin CXXDEFS)" "environment" +-CXXDEFS= -D__cplusplus +-endif +- +-ifneq "$(origin AR)" "environment" +-AR = ar +-endif +- +-ifneq "$(origin ARFLAGS)" "environment" +-ARFLAGS = rvs +-endif +- +-ifneq "$(origin LDFLAGS)" "environment" +-LDFLAGS = +-endif ++CC ?= cc ++CXX ?= g++ ++CXXFLAGS ?= ++CXXDEFS = -D__cplusplus ++AR ?= ar ++ARFLAGS ?= rvs + + #### Delete default suffix rules + .SUFFIXES: +@@ -359,13 +326,13 @@ $(PROGS): + cd $(LOCAL_OBJ); \ + if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + else \ + cd $(LOCAL_OBJ); \ + if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + fi ; + +diff --git a/src/c_make.glm b/src/c_make.glm +index 0decc17..b82131c 100644 +--- a/src/c_make.glm ++++ b/src/c_make.glm +@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen + + SUBDIRS = Common ICM Glimmer Util + +-CFLAGS = -g -Wall +-CXXFLAGS = -g -Wall +- +-LDFLAGS = -g -lm ++LIBS = -lm + + + #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch new file mode 100644 index 000000000000..6eebc5610414 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch @@ -0,0 +1,196 @@ +diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex +--- glimmer3.02.old/docs/notes.tex 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/docs/notes.tex 2015-05-25 22:41:39.450340098 +0200 +@@ -306,7 +306,7 @@ + The script would then run the commands: + \BSV\begin{verbatim} + long-orfs -n -t 1.15 genom.seq run1.longorfs +- extract -t genom.seq run1.longorfs > run1.train ++ glimmer_extract -t genom.seq run1.longorfs > run1.train + build-icm -r run1.icm < run1.train + glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1 + \end{verbatim}\ESV +@@ -330,9 +330,9 @@ + \end{verbatim}\ESV + The script would then run the commands: + \BSV\begin{verbatim} +- extract -t genom.seq train.coords > run2.train ++ glimmer_extract -t genom.seq train.coords > run2.train + build-icm -r run2.icm < run2.train +- upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream ++ upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream + elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif + set startuse = `start-codon-distrib -3 genom.seq train.coords` + glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2 +@@ -358,11 +358,11 @@ + The script would then run the commands: + \BSV\begin{verbatim} + long-orfs -n -t 1.15 genom.seq run3.longorfs +- extract -t genom.seq run3.longorfs > run3.train ++ glimmer_extract -t genom.seq run3.longorfs > run3.train + build-icm -r run3.icm < run3.train + glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1 + tail +2 run3.run1.predict > run3.coords +- upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream ++ upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream + elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif + set startuse = `start-codon-distrib -3 genom.seq run3.coords` + glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3 +@@ -1081,12 +1081,12 @@ + \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords} + \eq + +-\subsubsection{\Pg{extract} Program} ++\subsubsection{\Pg{glimmer_extract} Program} + This program reads a genome sequence and a list of coordinates + for it and outputs a multi-fasta file of the regions specified + by the coordinates. Output goes to standard output. + \bq +- \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords} ++ \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords} + \eq + + \subsubsection{\Pg{multi-extract} Program} +diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh +--- glimmer3.02.old/sample-run/g3-from-scratch.csh 2006-06-12 21:46:35.000000000 +0200 ++++ glimmer3.02/sample-run/g3-from-scratch.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -50,7 +50,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh +--- glimmer3.02.old/sample-run/g3-from-training.csh 2006-06-12 21:46:35.000000000 +0200 ++++ glimmer3.02/sample-run/g3-from-training.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -42,7 +42,7 @@ + step1: + # Extract the training sequences from the genome file + echo "Step 1 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $coords > $tag.train ++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -66,7 +66,7 @@ + # upstream of the start locations in $coords + echo "Step 3 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh +--- glimmer3.02.old/sample-run/g3-iterated.csh 2006-06-13 14:15:28.000000000 +0200 ++++ glimmer3.02/sample-run/g3-iterated.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -57,7 +57,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -103,7 +103,7 @@ + # upstream of the start locations in $tag.coords + echo "Step 6 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $tag.coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh +--- glimmer3.02.old/scripts/g3-from-scratch.csh 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/scripts/g3-from-scratch.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -50,7 +50,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh +--- glimmer3.02.old/scripts/g3-from-training.csh 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/scripts/g3-from-training.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -42,7 +42,7 @@ + step1: + # Extract the training sequences from the genome file + echo "Step 1 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $coords > $tag.train ++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -66,7 +66,7 @@ + # upstream of the start locations in $coords + echo "Step 3 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh +--- glimmer3.02.old/scripts/g3-iterated.csh 2006-06-13 14:15:46.000000000 +0200 ++++ glimmer3.02/scripts/g3-iterated.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -57,7 +57,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -103,7 +103,7 @@ + # upstream of the start locations in $tag.coords + echo "Step 6 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $tag.coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile +--- glimmer3.02.old/src/Util/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 +@@ -8,7 +8,7 @@ + SOURCES = $(UTIL_SRCS) + OBJECTS = $(UTIL_OBJS) + +-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \ ++PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \ + uncovered window-acgt + + LIBRARIES = +diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc +--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200 +@@ -297,7 +297,7 @@ + + { + fprintf (stderr, +- "USAGE: extract [options] <sequence-file> <coords>\n" ++ "USAGE: glimmer_extract [options] <sequence-file> <coords>\n" + "\n" + "Read fasta-format <sequence-file> and extract from it the\n" + "subsequences specified by <coords>. By default, <coords>\n" +--- glimmer3.02.old/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 ++++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile 2015-05-25 23:13:34.230372010 +0200 +@@ -21,7 +21,7 @@ + + entropy-score: entropy-score.o libGLMcommon.a + +-extract: extract.o libGLMcommon.a ++glimmer_extract: extract.o libGLMcommon.a + + multi-extract: multi-extract.o libGLMcommon.a + diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild new file mode 100644 index 000000000000..992a6d327fcb --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils toolchain-funcs + +MY_PV=${PV//./} + +DESCRIPTION="An HMM-based microbial gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/" +SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/${PN}${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-glibc210.patch + "${FILESDIR}"/${P}-jobserver-fix.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${PN}-3.02b-rename_extract.patch +) + +src_prepare() { + sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ + -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" + # Fix Makefile to die on failure + sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die + epatch "${PATCHES[@]}" +} + +src_compile() { + emake \ + -C src \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + AR=$(tc-getAR) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/test || die + dobin bin/* + + insinto /usr/share/${PN} + doins -r scripts + + dodoc glim302notes.pdf +} diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild new file mode 100644 index 000000000000..9653024a1de2 --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils toolchain-funcs + +MY_PV=${PV//./} + +DESCRIPTION="An HMM-based microbial gene finding system from TIGR" +HOMEPAGE="http://ccb.jhu.edu/software/glimmer" +SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="app-shells/tcsh + sci-biology/elph" + +#S="${WORKDIR}/${PN}${PV}" +S="${WORKDIR}/${PN}3.02" + +PATCHES=( + "${FILESDIR}"/${P}-jobserver-fix.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-rename_extract.patch +) + +src_prepare() { + sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ + -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" + # Fix Makefile to die on failure + sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die + # + sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die + sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die + sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die + sed -i "s/@ if/if/" src/c_make.gen || die + # avoid file collision on /usr/bin/extract #247394 + epatch "${PATCHES[@]}" +} + +src_compile() { + emake \ + -C src \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + AR=$(tc-getAR) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/test || die + dobin bin/* + + insinto /usr/share/${PN} + doins -r scripts + + dodoc glim302notes.pdf +} diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/glimmer/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest new file mode 100644 index 000000000000..a3814accc62d --- /dev/null +++ b/sci-biology/glimmerhmm/Manifest @@ -0,0 +1,6 @@ +AUX 3.0.1-gentoo.patch 4235 SHA256 04eef55bb0cdb4455d143bec7fd0113491caee72fa9a6c56237024b4f18abbf4 SHA512 e0350a4b604fe76462bbb7139264a9b2916c050c335589031bdca0cf0c6a653bbf84d9827f5c2096ff13f1007d4ef2e93698814758f787a98e4dd818be44bc3d WHIRLPOOL 890fd4dfdae05f846b9fe2fae239e68b90c80c7de8ae4f3449c340f99e25f93f9b0e3075756f61dc700c41b973e38b7147de518813d6012c5f640b7218487a59 +DIST GlimmerHMM-3.0.1.tar.gz 45475952 SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7 WHIRLPOOL f2cc0f6cea083c223273dd59f9474a054c049b697fc122925d4f5820170ade67bfa76c6dd218ab10be5675fe0a2a2a9fa5172be540509770332cc5a1d6862ff7 +EBUILD glimmerhmm-3.0.1-r1.ebuild 1190 SHA256 8aa3d25d87b788b27f2c8b2cab541f007dd8506e90137eac8d22bc86017cc1b1 SHA512 9faea51c07ef865eb0dfd9028077ef7a3e42a633ca39dd1a66caf817a35a75236ecda3ed58f9941bd18c925f43a4319e65f1f03510032bfe92f0cae81076dd9d WHIRLPOOL ca23ebcac4ba310cb55e935af13381bf2a93ebfffc65f01912e9bb78d1cacd8705b1f10ed3d5e2c9e89d882ca4b1b7ac9a64dd13fac8f89367de05687b9c1b70 +MISC ChangeLog 2472 SHA256 09afa0cb342126d3541311772971705a0f6f43f43db8e48354fb42cc2203c230 SHA512 d6ab119f62efb6da6d04015fdf0a4d5d7ad8bf664ed22e5908bb50dbe4b73f0e5062100da3175c6715452da03e268f7afc7f8825c5daa7b5c0a2154c555e179e WHIRLPOOL 7187e5733d044e31f78467c17c64badaf8e2d28b870cb8f7632d6d6ddf1962e6abaf110c8692902539cdfb213cc201562167c6ac6d7517f2019c7c5a7abf41ed +MISC ChangeLog-2015 1438 SHA256 139eecbffefb14e67a5ce60286592f4cffc6c854c800c4734d3d6cf317cf711f SHA512 afab9849cf3851d8059bcbb9b451e342a24c5e6c2a780d880c90af3d5ad8dbad293e7a6ae47dba17c2d11166e52f5785336f07a477c72a4603df91c758dacf76 WHIRLPOOL 02a8691b718b35451af167db293045ba823721ef7641223caec20a2c654043a836d908f3233d8dfa3ee9efcdf7445deddd3f56472767701bc414fbce5897d2b0 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch new file mode 100644 index 000000000000..949a4fe3e92d --- /dev/null +++ b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch @@ -0,0 +1,153 @@ + sources/makefile | 15 +++++-------- + train/makefile | 59 +++++++++++++++++++++++++++++++---------------------- + 2 files changed, 40 insertions(+), 34 deletions(-) + +diff --git a/sources/makefile b/sources/makefile +index f287d71..c560f48 100644 +--- a/sources/makefile ++++ b/sources/makefile +@@ -2,25 +2,22 @@ + + + +-CC=g++ +-CFLAGS=-g +- + all: glimmerhmm + + glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o +- $(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm + + glimmerhmm.o: glimmerhmm.c +- $(CC) $(CFLAGS) -c glimmerhmm.c ++ $(CXX) $(CXXFLAGS) -c glimmerhmm.c + + graph.o: graph.c +- $(CC) $(CFLAGS) -c graph.c ++ $(CXX) $(CXXFLAGS) -c graph.c + + sites.o: sites.c +- $(CC) $(CFLAGS) -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c + + tree_util_prob.o: tree_util_prob.c +- $(CC) $(CFLAGS) -c tree_util_prob.c ++ $(CXX) $(CXXFLAGS) -c tree_util_prob.c + + util.o: util.c +- $(CC) $(CFLAGS) -c util.c ++ $(CXX) $(CXXFLAGS) -c util.c +diff --git a/train/makefile b/train/makefile +index 2383f18..d5a7107 100644 +--- a/train/makefile ++++ b/train/makefile +@@ -2,9 +2,6 @@ + + # C compiler + +-C = gcc +-CC = g++ +-CFLAGS = -O1 ${SEARCHDIRS} + #CFLAGS = -O3 -g -Wall + LIBS = -lm + +@@ -15,64 +12,76 @@ all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco + + + misc.o: misc.c +- ${C} ${CFLAGS} -c misc.c ++ $(CC) $(CFLAGS) -c misc.c + + build-icm.o: build-icm.c +- ${C} ${CFLAGS} -c build-icm.c ++ $(CC) $(CFLAGS) -c build-icm.c + + build-icm: build-icm.o misc.o +- $(C) -o $@ build-icm.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS) + + build-icm-noframe.o: build-icm-noframe.c +- ${C} ${CFLAGS} -c build-icm-noframe.c ++ $(CC) $(CFLAGS) -c build-icm-noframe.c + + build-icm-noframe: build-icm-noframe.o misc.o +- $(C) -o $@ build-icm-noframe.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS) + + build1: build1.o +- ${CC} build1.c -o build1 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS) + + build2: build2.o +- ${CC} build2.c -o build2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS) + + falsecomp: falsecomp.o +- ${CC} falsecomp.c -o falsecomp $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS) + + findsites: findsites.o +- ${CC} findsites.c -o findsites $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS) + + karlin: karlin.o +- ${CC} karlin.c -o karlin $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS) + + score: score.o +- ${CC} score.c -o score $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS) + + score2: score2.o +- ${CC} score2.c -o score2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS) + + scoreATG: scoreATG.o +- ${CC} scoreATG.c -o scoreATG $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS) + + scoreATG2: scoreATG2.o +- ${CC} scoreATG2.c -o scoreATG2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS) + + scoreSTOP: scoreSTOP.o +- ${CC} scoreSTOP.c -o scoreSTOP $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS) + + escoreSTOP2: scoreSTOP2.o +- ${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS) + +-rfapp: erfapp.o +- ${CC} erfapp.c -o erfapp $(LIBS) ++erfapp: erfapp.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS) + + sites.o: sites.c +- ${CC} ${CFLAGS} -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c ++ ++scoreATG.o: scoreATG.c ++ $(CXX) $(CXXFLAGS) -c scoreATG.c ++ ++scoreSTOP.o: scoreSTOP.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP.c ++ ++scoreSTOP2.o: scoreSTOP2.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP2.c ++ ++scoreATG2.o: scoreATG2.c ++ $(CXX) $(CXXFLAGS) -c scoreATG2.c + + utils.o: utils.c +- ${CC} ${CFLAGS} -c utils.c ++ $(CXX) $(CXXFLAGS) -c utils.c + + splicescore.o: splicescore.c +- ${CC} ${CFLAGS} -c splicescore.c ++ $(CXX) $(CXXFLAGS) -c splicescore.c + + splicescore: splicescore.o sites.o utils.o +- ${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS) diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild new file mode 100644 index 000000000000..1d3cf1171d76 --- /dev/null +++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P=GlimmerHMM + +DESCRIPTION="A eukaryotic gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +src_unpack() { + unpack ${A} + mv GlimmerHMM ${P} +} + +src_prepare() { + sed \ + -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \ + -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \ + -i "${S}/train/trainGlimmerHMM" || die + + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CC CXX +} + +src_compile() { + emake -C "${S}/sources" + emake -C "${S}/train" +} + +src_install() { + dobin sources/glimmerhmm train/trainGlimmerHMM + + insinto /usr/share/${PN}/lib + doins train/*.pm + insinto /usr/share/${PN}/models + doins -r trained_dir/* + exeinto /usr/libexec/${PN}/training_utils + doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} + + dodoc README.first train/readme.train +} diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/glimmerhmm/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest new file mode 100644 index 000000000000..acd1a5e6c6f4 --- /dev/null +++ b/sci-biology/gmap/Manifest @@ -0,0 +1,5 @@ +DIST gmap-gsnap-2015-12-31.v5.tar.gz 4169874 SHA256 2317ba63578ba87f534689c0bf6930a9b177df4aa8a75b2a82f2118760ff3037 SHA512 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000000000000..82ae6f3f2748 --- /dev/null +++ b/sci-biology/gmap/gmap-2015.12.31.5.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit versionator + +MY_BASE_PV="$(replace_all_version_separators '-' $(get_version_component_range 1-3))" +MY_PV="${MY_BASE_PV}.v$(get_version_component_range 4)" + +DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" +HOMEPAGE="http://research-pub.gene.com/gmap/" +SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz" + +LICENSE="gmap" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/gmap-${MY_BASE_PV}" diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/gmap/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/goby-cpp/Manifest b/sci-biology/goby-cpp/Manifest new file mode 100644 index 000000000000..25cf02ed1b62 --- /dev/null +++ b/sci-biology/goby-cpp/Manifest @@ -0,0 +1,12 @@ +AUX Alignments.proto 26192 SHA256 0f70eb8db279b0dae72a2a59113d68f3151199aed655354532e135bb9325c191 SHA512 c5b67577bfd8432e64489dfb08333adcece8712a398497facb284b52c5b773eff79d71c6dc5bcb72ab21b977423530e27cac3fa2a888c3a00cca1a09faf1b00f WHIRLPOOL 937bc8d18dba2dfb747db3ed38e1d3b5c09cc4e2eedd1ea3edfe5d9128b0a096166b71db217d9ba097c2041ec948e09056e97321e22a2d5b9d4b2d24b3cfc83b +AUX Reads.proto 3128 SHA256 ca2cd55eadf9ad9e64111ebd461a78456223c781fad99c2705c37cbbeeee215d SHA512 eed972f7f054096ba0e4b215e1551b8acdee6024cec6091abe2b92e268b09fb77d2e9c2a90520611da3bfe37e69a8341e406c4eccb57b0c88f3664f7f2818e27 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d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/goby-cpp/files/Alignments.proto b/sci-biology/goby-cpp/files/Alignments.proto new file mode 100644 index 000000000000..fe7f56647644 --- /dev/null +++ b/sci-biology/goby-cpp/files/Alignments.proto @@ -0,0 +1,597 @@ +package goby; + +option java_package = "edu.cornell.med.icb.goby.alignments"; + +option optimize_for = SPEED; + +/* + This message is written to 'basename'.entries as a very large chunked collection. +*/ +message AlignmentCollection { + repeated AlignmentEntry alignment_entries = 1; +} + + +message AlignmentEntry { + /* Multiplicity of this entry. The number of times this alignment entry would be repeated exactly the same if + query redundancy had not been removed by read factorization. + */ + optional uint32 multiplicity = 7; + + /* + Compressed stream of data. Removed since Goby 2.0 supports chunk codecs. Do not reuse field index 23 + optional bytes compressed_data = 23; + */ + + /* An integer that uniquely identifies the query (a short read) in a set of alignment runs. When several + alignment runs are made with the same set of query sequences, equality of query index means that the query + sequences were the same. (Comparing integers for equality is much faster than comparing strings.) + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 query_index = 1; + /* An integer that uniquely identifies the target (e.g., a chromosome) in a set of alignment runs. When several + alignment runs are made with the same set of target sequences, equality of target index means that the target + sequence was the same across the runs. (Comparing integers for equality is much faster than comparing strings.) + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 target_index = 2; + /* + The position on the target of the start of the alignment between the query and the target. + In the following example, position is 3 because the third base of the query 'C' was aligned with + position 3 of the reference (two read bases were soft clipped: "ct"). This example shows that the + alignment can start at a mismatch if it was so constructed by the aligner. + + 0123456789 + AAAAGTCAAA target + ctCGTC query + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 position = 3; + + /* + True when the query matches the target on the reverse strand + */ + optional bool matching_reverse_strand = 6; + + /* + The position on the query where the alignment starts. This value is different from zero + when some bases/residues of the query could not be aligned with the target. + TODO: Rename this to left_trim. Add a right_trim property. + */ + optional uint32 query_position = 5; + + /* + The score of the alignment, where larger scores indicate better matches between the query and the target. + If an aligner outputs only the number of mismatches between query and target, the score is taken to be + -(#mismatches(query,target)). + */ + optional float score = 4; + + /* + Number of bases/residues that differ in the alignment between query and target sequences. + */ + optional uint32 number_of_mismatches = 8; + + /* + Cumulative number of insertions and/or deletions present in the alignment. + */ + optional uint32 number_of_indels = 9; + + /* + Number of bases that have been aligned for the query. Please note that query_aligned_length must be + less or equal to query_length. + */ + optional uint32 query_aligned_length = 11; + + /* + Number of bases that have been aligned for the target. + */ + optional uint32 target_aligned_length = 12; + + repeated SequenceVariation sequence_variations = 13; + + /* + Length of the query sequence. + */ + optional uint32 query_length = 10; + /* + Mapping Quality (phred-scaled posterior probability that the mapping + position of this read is incorrect). Please note that different aligners + may estimate mapping quality with different approaches, resulting in aligner + specific differences in the distribution of mapping quality. It is recommended + to condition mapping quality on the aligner that produced the specific alignment + being processed. See aligner name and version in the header. + Note that the following description is preliminary. A clear specification is + needed: + The mapping quality should be proportional to the + log of the probability that the given mapping is the "correct" one. + So if there are five equally good mappings of a read to the genome, + the probability of each would be 0.2, and the mapping quality would be + something like -10*log10(1-0.2) = 1. If a mapping is highly likely, + say a 1e-4 of it being wrong, then the mapping quality would be + -10*log10(1e-4) = 40. + */ + optional int32 mapping_quality = 14; + + /* + If this read was aligned with a pair, the flags for the pair alignment (based on SAM): + 000000001 paired + 000000010 properly paired + 000000100 read unmapped + 000001000 mate unmapped + 000010000 read reverse strand + 000100000 mate reverse strand + 001000000 first in pair + 010000000 second in pair + 100000000 not primary alignment + */ + optional uint32 pair_flags = 15; + + /* + If there is an alignment entry for the paired read (the paired read was mapped), a link to the entry is given. + */ + optional RelatedAlignmentEntry pair_alignment_link = 16; + + /* Index of the read fragment from which this alignment was obtained. */ + optional uint32 fragment_index = 17; + + /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more + alignment entries, one for each matching part of the read, and link these entries with + spliced_alignment_links. The field spliced_forward_alignment_link points to the next + AlignmentEntry in the chain of spliced alignments. + */ + optional RelatedAlignmentEntry spliced_forward_alignment_link = 18; + + /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more + alignment entries, one for each matching part of the read, and link these entries with + spliced_alignment_links. The field spliced_backward_alignment_link points to the previous + AlignmentEntry in the chain of spliced alignments. + */ + optional RelatedAlignmentEntry spliced_backward_alignment_link = 22; + + /* + If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two alignment entries, one for each + matching part of the read, and flag describes the spliced_alignment_link with these + binary flags: + 000000001 normal + 000000010 novel + */ + optional uint32 spliced_flags = 19; + + /* The size of the insert used when making the sequence library. This is the total size of the DNA + fragment to sequence, without the adapters. This is not the length of sequence that separates the reads. + See http://seqanswers.com/forums/showthread.php?t=8730 for details. Insert size is inferred for each pair + of reads by the aligner and is recorded here if was estimated (i.e., for paired-end reads). + */ + optional sint32 insert_size = 20; + + /* + The sample index. Uniquely identifies the aligned sample this read was read from. Storing the sample index in the + alignment entry makes it possible to concat alignments from different origins and track what sample originally + contained each entry. + */ + optional uint32 sample_index = 21; + /* + The total number of times the query index associated with this entry occurs across the entire alignment file. + + This field is used to purge queryIndex->smallIndex associations after all instances of a queryindex have + been seen (see QueryIndexPermutation class). When each entry has a value for this field, the header field + query_index_occurrences is true. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 query_index_occurrences = 25; + /* + The total number of times the read matches the reference across the entire alignment file. This differs from + query_index_occurrences because reads that are matching through splice and pair links count as one for ambiguity. + The field can be used to filter by ambiguity-threshold on the fly after an alignment has been done (to restrict + entries to more smaller thresholds). When each entry has a value for this field, the header field + ambiguity_stored_in_entries is true. + + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 ambiguity = 27; + /* + List of BAM attributes, if the alignment was imported from BAM. The attributes are stored in exactly the format + allowed for BAM. For instance, X0:i:9 X1:i:1 MD:Z:68 RG:Z:SRR084825 will be stored as four strings: + "X0:i:9", "X1:i:1", "MD:Z:68", "RG:Z:SRR084825". Note that sam-to-compact will interpret some BAM attributes + and populate goby native fields. Such tags do not appear in bam_attributes, and are instead re-generated from + the corresponding goby native fields. + Since Goby 2.0. + */ + repeated string bam_attributes = 50; + /* + Quality scores for all bases of the read. + Since Goby 2.0. + */ + optional bytes read_quality_scores = 55; + + /* + Origin index. An integer that references a ReadOriginInfo message in the alignment header and + makes it possible to track the origin of the read (especially useful after several alignments + have been merged/concatenated). + (Since Goby 2.0). + */ + optional uint32 read_origin_index = 26; + /* + Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially + erroneous bases, or bases that belong to a different part of the reference genome. Left clipped bases are + stored in this field as character bases, or as an equal sign character '=' when the clipped base did match + the reference base. For instance "A=G" for three soft-clipped bases, the middle one matching the genome at + this position. The number of bases in softClippedBasesLeft is exactly equal to queryPosition. + */ + optional string softClippedBasesLeft = 30; + /* + Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially + erroneous bases, or bases that belong to a different part of the reference genome. Right clipped bases are + stored in this field as character bases, or as an equal sign character '=' when the clipped base did match + the reference base. The number of bases in softClippedBasesRight is exactly equal + to queryLength - queryAlignedLength - queryPosition. + */ + optional string softClippedBasesRight = 31; + + /* + Quality scores for bases in softClippedBasesLeft. Stored in Phred Units. + */ + optional bytes softClippedQualityLeft = 32; + /* + Quality scores for bases in softClippedBasesRight. Stored in Phred Units. + */ + optional bytes softClippedQualityRight = 33; + /* + Sequence for a read placed near this entry, but unmapped to the reference sequence. For instance, used to record + the sequence of a mate that did not map to the reference. We know that the mate maps in the proximity of this entry + (it is placed) but are unable to map it to a specific genomic position. The sequence is always given as obtained + from the reads file. + */ + optional string placedUnmappedSequence=40; + /* + Quality scores for a read placed near this entry. Phred units. + */ + optional bytes placedUnmappedQuality=41; + + /* + Read name. In SAM/BAM this is referred to as QNAME. Paired and segmented reads will have the same Read name. + */ + optional string readName=42; +} + +/* A link to another alignment entry. This message type is used to represent relations + between alignments, such as the relation between the two read fragments in a paired-end protocol, + or the relation between parts of reads that align through an exon exon junction and map in + different locations of the genome. + */ +message RelatedAlignmentEntry { + /* Target index of the location where the other alignment entry is mapped. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 target_index = 1; + + /* Position on the reference where the other alignment entry is mapped. * + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 position = 2; + + /* Index of the fragment for the related alignment entry. This index + makes it possible to identify which of the read fragments mapped to the given + location is related to the source alignment entry. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 fragment_index = 3; + + optional uint32 optimized_index=50; +} + +/* + Represents sequence variations between the query and the reference sequences. Many variations can be represented. + For instance, an insertion at position 5 in the reference would be represented as from="A", to="" position=5. + A mutation T->G at position 6 would be rendered as from="T", to="G" position=6. Padded alignments (see SAM description) + can be described by a combination of pair-wise alignments, where the gap character '-' is used to indicate that no + base exists in the sequence considered for the alignment position, for instance: + + - Padding example: + + 123 (<-positions) +ref A-C + A-T [from="-" to="" position=2] [from="C" to="T" position=3] + ACT [from="" to="C" position=2] [from="C" to="T" position=3] + A-T [from="-" to="" position=2] [from="C" to="T" position=3] + + - Mutation example: + 123 (<-positions) +ref ATT + ACT [from="T" to="C" position=2] + + -- Example of deletion in a read: + 123 (<-positions) +ref ATT + A-T [from="T" to="-" position=2] + + -- Example of insertion of two base pairs in a read: + 12345 (<-positions) +ref A--TT + ACCTT [from="" to="CC" position=2] + + */ +message SequenceVariation { + /* The reference bases. Can include one or more gap characters '-', to indicate that the reference sequence has + no base at this alignment position. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional string from = 2; + /* The read bases that differ from the reference sequence. Can include one or more gap characters '-', to indicate + that the query sequence has no base at this alignment position. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional string to = 1; + /* + The position of the variation on the read, as if the read always matched on the forward strand. + Adding position to the index where the reference starts aligning the read yields the position of the variation + in reference/target sequence space. Since position starts at one the resulting position will also be one based. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 position = 3; + /* + The position of the variation, starting from the beginning of the aligned read (position 1), and up to the length + of the read (inclusive). Use this index if you need to know how far the variation is observed from the beginning + of the sequenced read. When the read has an insertion, this index records the position immediately before the base + where the bases are inserted (these bases are in the to field). + When the read has a deletion, read_index records the position in the read after which the bases that would align + in the reference are missing (these bases are in the from field). + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 read_index = 5; + + /** + The read base quality scores for those bases that are given in the to field. This field + is populated when the reads used to perform the search include quality scores, and when + the alignment parser can extract the information from the aligner's output. + (this option is currently not implemented in Goby.) + */ + optional bytes to_quality = 4; + +} +/* + This message is written to 'basename'.header +*/ + +message AlignmentHeader { + /* + The smallest possible query index in this alignment. Data stored as an array where + queryIndex is the array index will be stored with only the elements in the inclusive + range [smallestSplitQueryIndex largestSplitQueryIndex] + Such data structures include queryLength and some arrays in the TooManyHits data + structure. + */ + optional uint32 smallest_split_query_index = 9; + /* + The largest possible query index in this alignment. Data stored as an array where + queryIndex is the array index will be stored with only the elements in the inclusive + range [smallestSplitQueryIndex largestSplitQueryIndex] + Such data structures include queryLength and some arrays in the TooManyHits data + structure. + */ + optional uint32 largest_split_query_index = 11; + + /* Mapping from query identifier name to query index (as used in alignment entries). + */ + optional IdentifierMapping query_name_mapping = 1; + + /* Mapping from target identifier name to target index (as used in alignment entries). + */ + optional IdentifierMapping target_name_mapping = 2; + + /* + The number of query sequences + */ + optional uint32 number_of_queries = 5; + /* + The number of target sequences + */ + optional uint32 number_of_targets = 6; + /* + The number of reads that were aligned to the reference and are represented in this alignment archive. + */ + optional uint32 number_of_aligned_reads = 7; + + /* + Length of the query sequences. One number per query, in the order of increasing query index. + This information has been moved to the individual alignment entries. + */ + repeated uint32 query_length = 3 [deprecated = true]; + /* + If query length is constant across all the queries, this field contains the constant length. + In such cases, query_length will be empty. + */ + optional uint32 constant_query_length = 10; + + /* + Length of the target sequences. One number per target, in the order of increasing target index. + The target indexes must be 0..(number of targets - 1). + */ + repeated uint32 target_length = 8; + /* + Indicates whether this alignment is sorted by position. True: the alignment entries occur in sorted + order, such that entry a occurs before entry b if a.targetIndex< b.targetIndex or, when entries + have the same target, when a.position < b.position. + */ + optional bool sorted = 13; + + /* + Indicates whether this alignment is indexed by position. When this attribute is true, a file called + 'basename'.index exists that contains the AlignmentIndex message (GZip compressed). + */ + optional bool indexed = 14; + /* + True when query lengths are stored in alignment entries (Goby 1.7+). + */ + optional bool query_lengths_stored_in_entries = 15; + /* + Name of the aligner that produced this alignment. + */ + optional string aligner_name = 17; + /* + Version number for the aligner implementation that produced this alignment. + */ + optional string aligner_version = 18; + /* + The version of Goby that created this alignment file. + */ + optional string version = 25; + + /* + Sample basenames, in the order of increasing sampleIndex, starting with sampleIndex=0. + */ + + repeated string sample_basename = 30; + + /* + This field is true when the query indices of alignment entries were permuted to smaller indices. Only sorted + alignments can have query_indices_were_permuted=true. When the field is true, and you need to retrieve the + original query-index of an alignment (because you want to retrieve the specific read(s) from a read file for + instance), you will need the information in the permutation file (extension basename.perm) and transform back + each small index of interest to the original query index. + */ + optional bool query_indices_were_permuted = 26; + /* + This field is true when entries in the alignment .entries file all have the query_index_occurrences field populated + (Since Goby 2.0). + */ + optional bool query_index_occurrences = 35; + + /* + This field is true when entries in the alignment .entries file all have the ambiguity field populated + (Since Goby 2.0). + */ + optional bool ambiguity_stored_in_entries = 36; + /* + This field is true when entries in the alignment .entries file all have the read_quality_score field populated. + (Since Goby 2.0). + */ + optional bool all_read_quality_scores = 40; + /* + A description of the origin of sets of reads. Serves a similar function to BAM read groups, but more flexible and + efficient. Instead of storing strings, we use integers in the entries. + Alignemnt entries will link to a specific ReadOriginInfo with the origin_index field. + (Since Goby 2.0). + */ + repeated ReadOriginInfo read_origin = 27; +} + +message IdentifierMapping { + repeated IdentifierInfo mappings = 1; +} + +message IdentifierInfo { + required string name = 1; + required uint32 index = 2; +} + + +/* + A description of the origin of sets of reads. Stored in the Goby alignment header and linked + from alignment entries. Goby makes it possible to adapt origin equivalence rules on the fly + efficiently. To do this, it is sufficient to read the header of the alignment, decide which + ReadOriginInfo instances are equivalent (e.g., by looking at sample, platform, library, or + other fields in the message), then construct a function e(a):int. This function takes + one originIndex parameter and returns another integer that maps to an equivalent class. The + equivalence class can be used to estimate error models for entries that belong to each class, + for instance. + (Since Goby 2.0). + */ +message ReadOriginInfo { + /* + Origin index. An integer that links alignment entries to their origin information. + */ + required uint32 origin_index = 1; + /* + Identifier that describes the origin of the reads. This field is compatible with the ID/platform field of BAM read + groups. Free text. + */ + required string origin_id = 2; + /* + The sample from which the reads were sequenced. This field is compatible with the SM/sample field of BAM read + groups. Free text. + */ + optional string sample = 4; + /* + The platform on which the reads were sequenced. This field is compatible with the PL/platform field of BAM read + groups. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO. + */ + optional string platform = 5; + /* + The library from which the reads were sequenced. This field is compatible with the LB/library field of BAM read + groups. Free text. + */ + optional string library = 8; + /* + The platform unit on which the reads were sequenced. This field for compatibility with samtools. + */ + optional string platform_unit = 12; + /* + The date the reads were sequenced. Useful to identify batch effects, in the format dd:MMM:yyyy. + The month is Jan, Feb, etc. to avoid all confusion with days when day<=12. + */ + optional string run_date = 6; +} + +/* + This message is written to 'basename'.tmh +*/ + +message AlignmentTooManyHits { + /* + The threshold used by the aligner to determine that a query is ambiguous and should be dropped. + Referred to as parameter k below. + */ + required uint32 aligner_threshold = 2; + /* + The hits that are assigned to several (>k) reference location. + */ + repeated AmbiguousLocation hits = 1; + +} + +message AmbiguousLocation { + /* + The index of the query that matched too many times. + */ + required uint32 query_index = 1; + /* + The number of hits that triggered membership in the too many hits list. The query may hit more + locations than reported here, since some alignment tools will just drop queries that match above + a threshold and stop counting. This number can be >=k. + */ + required uint32 at_least_number_of_hits = 2; + /** +The length of the part of the query sequence that could be matched to the target (also called depth). +May be less than the length of the query sequence, in which case the match was not perfect. When merging +alignments produced by searching different reference sequences, consider only at_least_number_of_hits +from alignments that have exactly the longer depth for the query. */ + optional uint32 length_of_match = 3; +} + +/* + This message is written to 'basename'.index + */ +message AlignmentIndex { + /* + Stores one element by target sequence. Each element is the cumulative target length for the target + stored at index i. Assume there are four target sequences, with lengths {10, 12, 15, 34}. The field + targetPositionOffsets will contain: {0,10,22,37}. Such offsets can be used to calculate the absolute + position of a genomic location. Given targetIndex and positionOnReference, the absolute location + is defined as targetPositionOffsets[targetIndex]+positionOnReference. + */ + repeated uint32 target_position_offsets = 1 [packed = true]; + /* + The byte offsets into the compressed entries file. Byte offsets are matched with absolute position + by index. There should be as many elements in offsets as there are in absolutePosition + where chunks start which represent entries whose absolute positions are less than + */ + repeated uint64 offsets = 2 [packed = true]; + /* + The absolute positions of the first entry in the chunk that immediately start at offset. One element + per chunk in the 'basename'.entries file. + */ + repeated uint64 absolute_positions = 3 [packed = true]; + +} diff --git a/sci-biology/goby-cpp/files/Reads.proto b/sci-biology/goby-cpp/files/Reads.proto new file mode 100644 index 000000000000..32c1244a3eb3 --- /dev/null +++ b/sci-biology/goby-cpp/files/Reads.proto @@ -0,0 +1,96 @@ +package goby; + +option java_package = "edu.cornell.med.icb.goby.reads"; +option optimize_for = SPEED; + +message ReadCollection { + repeated ReadEntry reads = 1; +} + +message ReadEntry { + /* + Index of a read. + */ + required uint32 read_index = 1; + /* + Index of the barcode, if any. + */ + optional uint32 barcode_index = 10; + /* + Read identifier/name may be present. + */ + optional string read_identifier = 23; + /* + Additional description about the read (from Fasta/Q format). + */ + optional string description = 22; + /* + Length of the sequence. + */ + required uint32 read_length = 2; + /* + Sequence, encoded as ascii characters stored in single bytes. + */ + optional bytes sequence = 3; + /* + The second sequence in a pair. Stored the same way as the sequence attribute. + */ + optional bytes sequence_pair = 5; + /* + Length of the second sequence in a pair. + */ + optional uint32 read_length_pair = 6; + /* + Quality scores in Phred units, stored as single bytes (0-255). + */ + optional bytes quality_scores = 4; + /* + Quality scores for the second sequence in a pair. Stored as the 'qualityScores' attribute. + */ + optional bytes quality_scores_pair = 7; + /* + Compressed stream of data. The first byte indicates the compression/decompression method (codec). The remaining bytes are + content compressed with the codec. + */ + optional bytes compressed_data = 8; + /* + Stores meta-data about the reads. Typically meta-data is stored in the very first read of a + read collection, with the understanding that the meta-data applies to all the reads in the + collection. Meta-data can be used to store information about when the sample was sequenced, + or other information of interest. The key-value pair format is sufficiently flexible to + accomodate a variety of needs. The following keys are pre-defined. Please use pre-defined + keys so that automated tools can use metadata in relatively standard way. Please note that + some keys provide a format for the value. This format should also be followed to garantee + that meta data can be used computationally in fully automatic manner. + + key="sequencing-run-start-date" value="MM/DD/YYYY" Used to record when the sequencing run + was initiated on the instrument. Can be used to detect batch effect in a large set of samples. + key="platform" value="<free-text>". Value is free text, but the following terms are pre-defined. + Illumina GaIIx + Illumina HiSeq 1000 + Illumina HiSeq 2000 + Helicos Heliscope + LifeTech 5500 SOLiD + LifeTech 5500xl SOLiD + Roche 454 GS FLX Ti + + key="organism" value="species name" + Since Goby 1.9.1 + */ + repeated MetaData meta_data = 25; + +} +/* + A message to store a key/value pair and represent metadata about reads. + Since Goby 1.9.1 + */ +message MetaData { + /* + Provides the key. See examples in the documentation of meta_data for ReadEntry. + */ + required string key=1; + /* + Describes the value associated with the key. See examples in the documentation of meta_data for ReadEntry. + */ + required string value=2; +} diff --git a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch new file mode 100644 index 000000000000..415785466af7 --- /dev/null +++ b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch @@ -0,0 +1,16 @@ + src/Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/Makefile.am b/src/Makefile.am +index 1033382..33ca906 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -84,7 +84,7 @@ GobyReadsStats_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_D + GobyReadsStats_SOURCES = \ + GobyReadsStats.cc + +-GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} ++GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} -lz + GobyFastaToCompact_SOURCES = \ + GobyFastaToCompact.cc + diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild new file mode 100644 index 000000000000..1d9228d799dc --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=">=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/goby_${PV}/cpp" + +src_prepare() { + eautoreconf +} diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild new file mode 100644 index 000000000000..5bd75260414e --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=">=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/goby_${PV}/cpp" + +src_prepare() { + eautoreconf +} diff --git a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild new file mode 100644 index 000000000000..fcf8971fceb0 --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + >=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${PV}/cpp" + +PATCHES=( + "${FILESDIR}"/${P}-underlinking.patch +) + +src_prepare() { + sed \ + -e '/BUILD_TIMESTAMP/s:\(goby/timestamp.h\):$(top_srcdir)/src/\1:g' \ + -i src/Makefile.am || die + + pushd src/goby > /dev/null || die + cp "${FILESDIR}"/*.proto . || die + protoc --cpp_out=. *.proto || die + popd > /dev/null || die + + autotools-utils_src_prepare +} diff --git a/sci-biology/goby-cpp/metadata.xml b/sci-biology/goby-cpp/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/goby-cpp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest new file mode 100644 index 000000000000..678f78558ab7 --- /dev/null +++ b/sci-biology/goby/Manifest @@ -0,0 +1,9 @@ +DIST goby_1.9.7.3-deps.zip 19959489 SHA256 3932c61f001fc1d06ef298043d5206041e47175fa28d755efd01148de35b567a SHA512 a077e18d6bb7603522108de2b3c50d1b7a281c9e1a8d5d78c85b660285d743baf7b52ceaea44903a5a27adfa80ea5823d5aaa47a3f2ec426e7ddb17fd67a477d WHIRLPOOL 35f09d7a64c32358e6f4c4f8002e2569f2b79a019c9f111c5dd046860c26905baf8de8ee6bc7ebdd90b96c390f0202a4cd0487d4e84522b8f304bf9739696ba6 +DIST goby_1.9.7.3-src.zip 15642000 SHA256 fe32a6720fcc0858811e40b744c9bcfffbb6cf277be50102446ff8798fd9ab24 SHA512 f213908e745e6c6d86895412f3ad14a8e0f2f3fbaba9205bffd7415982fc53181ca0b03b543063d0cbcd87f881d1b58eedb38a5090fa7ac20bdc513e54f83dd5 WHIRLPOOL c5f0d7d21624983f9e6f95c65eb477a21b3d5749cca53dab537060c8ce0facf6b4cc1f2705af025088fb6fd325539907a53691f42fbdaa9f3044fae75bcaa8ce +DIST goby_1.9.8.1-deps.zip 20820943 SHA256 eb11916408a7978a1e90967783b8167b96c6d0dd60ae58cf1dab915a519d1bbb SHA512 16cf79e2dab8cfc62f9d012b88b0d81e712e67cf2f70582969624a019863f21ee20a4ce0517d5b74782d8d200318451e3f889fb967c6935e896d526d2a6fc02e WHIRLPOOL 00ec51b2999cb34b725a48ad0456d23c40a952272f58b558c8fb0cc3e086a89a11bd6440bddddb0ea7b9bbcadeb05078161b02617ee5c55baf388aa73802b187 +DIST goby_1.9.8.1-src.zip 15748880 SHA256 e2489a815a38bd10b1ec59b4e262a023f97994d9953f97bcc6571cadd05919c3 SHA512 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7d7909e5632e5d2c18241237d5e06501e50d2d1fe07a618e8a028fbdd17bc2a420e23bead1529c6cfe76a82fdb04fd636b911230b57722ad9bd16e796baeb87e WHIRLPOOL bbb96e4a38e1fef9c9f1acc80f6b895134f533ef9d6623584f247637e657c520a8937d002978fd8f7b652feda2321b7c1d194a3b27d8bdc28fabde57bedbf033 diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild new file mode 100644 index 000000000000..9cab1b56d54e --- /dev/null +++ b/sci-biology/goby/goby-1.9.7.3-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby" +EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2" +EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar" + +JAVA_ANT_REWRITE_CLASSPATH="true" + +#inherit java-pkg-2 java-ant-2 subversion +inherit java-pkg-2 java-ant-2 + +MY_P="${PN}_${PV}" + +DESCRIPTION="A DNA sequencing data management framework" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip + http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="+cpp" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPS="dev-java/commons-logging + dev-java/commons-lang:2.1 + dev-java/commons-io:1 + dev-java/protobuf-java:0 + dev-java/fastutil:0 + dev-java/log4j + dev-java/jsap + dev-java/commons-configuration + dev-java/commons-math:2" +DEPEND=">=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS} + cpp? ( ~sci-biology/goby-cpp-${PV} )" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i '/sge/ d' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar goby*.jar + java-pkg_dolauncher goby --jar goby.jar + + insinto /usr/share/${PN} + doins -r python + dodoc CHANGES.txt +} diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild new file mode 100644 index 000000000000..9cab1b56d54e --- /dev/null +++ b/sci-biology/goby/goby-1.9.8.1-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby" +EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2" +EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar" + +JAVA_ANT_REWRITE_CLASSPATH="true" + +#inherit java-pkg-2 java-ant-2 subversion +inherit java-pkg-2 java-ant-2 + +MY_P="${PN}_${PV}" + +DESCRIPTION="A DNA sequencing data management framework" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip + http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="+cpp" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPS="dev-java/commons-logging + dev-java/commons-lang:2.1 + dev-java/commons-io:1 + dev-java/protobuf-java:0 + dev-java/fastutil:0 + dev-java/log4j + dev-java/jsap + dev-java/commons-configuration + dev-java/commons-math:2" +DEPEND=">=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS} + cpp? ( ~sci-biology/goby-cpp-${PV} )" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i '/sge/ d' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar goby*.jar + java-pkg_dolauncher goby --jar goby.jar + + insinto /usr/share/${PN} + doins -r python + dodoc CHANGES.txt +} diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml new file mode 100644 index 000000000000..a1e19f7893ca --- /dev/null +++ b/sci-biology/goby/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="cpp">Compile C/C++ API</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest new file mode 100644 index 000000000000..0483bcfe2070 --- /dev/null +++ b/sci-biology/hmmer/Manifest @@ -0,0 +1,11 @@ +AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 SHA256 d1d2dd37606e512016a2e36cb1869433162b937e2a01d7d32ec755b913f3fc27 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f WHIRLPOOL bfd161f040aed24b327f1ce9a5f90a02bc79baf0c114819964c6f687a2602df98b8eab5e0471c75af8d58084da58b705b2398fc7ef8023b8b3002758dcfa0c69 +AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 SHA256 9c3b581704d410a2ac25b31816c179388092c04f034afcf4dbd59216951bdc00 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9 WHIRLPOOL 68f3ad01d6f91a1d26ffaaf0e6af299cb35181f7576eb9431a7b6aa7b5e9558c482d2cca47177fa21bef59b00ed7f06b5085109f57552bd844097d42bfbd0d82 +AUX hmmer-3.1_beta2-fix-header-install-path.patch 3202 SHA256 4d27d42010878a6cd21ea04921c85ea4ee08c1a21da68dc0b7a1fafbfaf3c6c5 SHA512 ccaaff25a50a60526d0a16196b2b1d8cd57a7e9d016ce2b6b36ba1c0123966113b10965303dceb494810cd17a802514bba3a49d010ee6bbdc039715b84524d9a WHIRLPOOL 8d909ebd0445d6f2fb75c7b71df942fdb5631b75602ac44840c632e5ccd9c7b4cc47172f4b3c8223fa9ee44e995233b93b8c0e1b55f5770cc268b29091e8ab45 +AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 SHA256 a0cc39baaf73280585ecf98b950fc96a432a0fbf956cbcbe60557c23b9d97d61 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff WHIRLPOOL df90c8d77165ccf529917003236c831826757927ae23b730411f29d5e7e1e48b9af6c94b56007c836be9f7cb744a6ef0f2fcb2d3141a4673155983f1469040b5 +DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 WHIRLPOOL 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SHA512 fdc4c77b49d32f5d767a351d09faca6c9229d0a58060514fcf9a455a50d6649b016d71269874e9de4ecd7a121a1bfa9c84f493641beb39f0da43d87155f15c6a WHIRLPOOL 91f2a297e642b06460ce950486bba9e20b06061d538d143a94465b794ea6b5c41cbc2655d7f4aa1f477ab39d24153bf02afddc3878f3089e27ee4effa6f9ea43 +MISC ChangeLog 3721 SHA256 00cdef946de218c91cb088cfc76f2b00a75b5c00e348cce7b6ad6a57c2bc7586 SHA512 b63a10d874eca6459e2f02e4b725fc0663fe8f900ce95ff46e53eb4fbd9a043c569529972497a8d374e5f9929997026d04c40046ecb1ccda8c8c5aa8811717db WHIRLPOOL 94b722a856e6edaf1ba85722a8cdcc65ae047ae2cae0f530dc7d18a806d94accbcbf1e0e65d195608c5d7201f93a1e544287a5e202d1989616f5f9d2d2c8fee5 +MISC ChangeLog-2015 5411 SHA256 6c0efb04e2ef19c016477e9f09f43844dbfa6561d0a30017788970911add7c8d SHA512 119f27f43cb815065b027d436f8e8ef81633cfb918327ff989f60728442f116ce00609e2cb8d4842b1430dd7dbea04927edb1c736217a4c59470a09a65a5c07e WHIRLPOOL c4503f79cfeef60de665e55f3138c1e261073e5751842a4fc51b0a3c70f1d9302bfd51bc97a762a6723777f1737879caddef85f582a314310932cfdf447961b7 +MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch new file mode 100644 index 000000000000..110c61f11821 --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch @@ -0,0 +1,22 @@ +Make the build system respect DESTDIR, in order to allow staged builds. + +--- a/Makefile.in ++++ b/Makefile.in +@@ -109,13 +109,13 @@ + # installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1) + # Creates these directories if they don't exist. + install: +- mkdir -p ${BINDIR} +- -mkdir -p ${MANDIR}/man${MANSUFFIX} ++ mkdir -p ${DESTDIR}${BINDIR} ++ -mkdir -p ${DESTDIR}${MANDIR}/man${MANSUFFIX} + for file in $(PROGS) $(PVMPROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file ${DESTDIR}$(BINDIR)/;\ + done + -for file in hmmer $(PROGS); do\ +- $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ ++ $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ + done + + # uninstall: Reverses the steps of "make install". diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch new file mode 100644 index 000000000000..783d0530aa7a --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch @@ -0,0 +1,108 @@ +* Fix ancient perl 4 modules that are long gone. +* Fix perl shebangs to be portable and usable on Prefix. +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/squid/Testsuite/bug-1-sfetch-paths ++++ b/squid/Testsuite/bug-1-sfetch-paths +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test for bug #1: sfetch/SSI path bug. + # sfetch can't follow paths out of current directory if it's using +--- a/squid/Testsuite/x-base-afetch ++++ b/squid/Testsuite/x-base-afetch +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-alistat ++++ b/squid/Testsuite/x-base-alistat +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-seqstat ++++ b/squid/Testsuite/x-base-seqstat +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-sfetch ++++ b/squid/Testsuite/x-base-sfetch +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-shuffle ++++ b/squid/Testsuite/x-base-shuffle +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-sindex ++++ b/squid/Testsuite/x-base-sindex +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-sreformat ++++ b/squid/Testsuite/x-base-sreformat +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/testsuite/sqc ++++ b/testsuite/sqc +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # sqc + # quality control script for exercising code, regression testing, +@@ -176,12 +176,11 @@ + # SRE, Tue Aug 6 11:16:39 2002 + # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $ + +-require "getopts.pl"; +-require "importenv.pl"; ++use Getopt::Std; + + # Parse our command line + # +-&Getopts('mp:r:v'); ++getopts('mp:r:v'); + if ($opt_m) { $do_memtest = 1; } + if ($opt_p) { push @prepdirs, $opt_p; } + if ($opt_r) { push @olddirs, $opt_r; } +@@ -506,7 +505,7 @@ + # + sub tempname { + my ($dir, $name, $suffix); +- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} + + foreach $suffix ("aa".."zz") { + $name = "$dir"."sre".$suffix.$$; +--- a/testsuite/test1-conversion.pl ++++ b/testsuite/test1-conversion.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test hmmconvert. + # diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch new file mode 100644 index 000000000000..b9ff5b92b8f9 --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch @@ -0,0 +1,89 @@ +Install headers into 'hmmer3' subdir and not into global includedir. + +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -465,11 +465,12 @@ + ${INSTALL} -d ${DESTDIR}${bindir} + ${INSTALL} -d ${DESTDIR}${libdir} + ${INSTALL} -d ${DESTDIR}${includedir} ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + ${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/ + for file in ${HDRS}; do\ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done +- ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/ ++ ${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/ + ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install + + # "make uninstall" reverses the steps of "make install" +--- a/Makefile.in ++++ b/Makefile.in +@@ -143,6 +143,7 @@ + ${INSTALL} -d ${DESTDIR}${bindir} + ${INSTALL} -d ${DESTDIR}${libdir} + ${INSTALL} -d ${DESTDIR}${includedir} ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + ${INSTALL} -d ${DESTDIR}${man1dir} + ${INSTALL} -d ${DESTDIR}${pdfdir} + ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install +--- a/src/impl_dummy/Makefile.in ++++ b/src/impl_dummy/Makefile.in +@@ -152,8 +152,9 @@ + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done + + uninstall: +--- a/src/impl_sse/Makefile.in ++++ b/src/impl_sse/Makefile.in +@@ -155,8 +155,9 @@ + + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done + + uninstall: +--- a/src/impl_vmx/Makefile.in ++++ b/src/impl_vmx/Makefile.in +@@ -152,8 +152,9 @@ + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done + + uninstall: +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -322,15 +322,16 @@ + ${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS} + + install: ++ ${INSTALL} -d ${DESTDIR}${includedir}/hmmer3 + ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install + for file in ${PROGS}; do \ + ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\ + done + ${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/ + for file in ${HDRS}; do \ +- ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\ + done +- ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\ ++ ${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\ + + uninstall: + ${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch new file mode 100644 index 000000000000..39fdbd50e457 --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch @@ -0,0 +1,331 @@ +Fix perl shebangs to be portable and usable on Prefix. +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/easel/demotic/infernal_tab2gff.pl ++++ b/easel/demotic/infernal_tab2gff.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic
++#!/usr/bin/env perl +
+ # TAJ 6/23/08 last mod 7/10/08
+ # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format
+--- a/easel/demotic/test.pl ++++ b/easel/demotic/test.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_blast; + +--- a/easel/devkit/rmanprocess.pl ++++ b/easel/devkit/rmanprocess.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # rmanprocess.pl <rman LaTeX2e output> + # +--- a/easel/miniapps/esl-afetch.itest.pl ++++ b/easel/miniapps/esl-afetch.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Testing the esl-afetch miniapp + # +--- a/easel/miniapps/esl-alimanip.itest.pl ++++ b/easel/miniapps/esl-alimanip.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-alimanip miniapp. + # +--- a/easel/miniapps/esl-alimap.itest.pl ++++ b/easel/miniapps/esl-alimap.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-alimap miniapp. + # +--- a/easel/miniapps/esl-alimask.itest.pl ++++ b/easel/miniapps/esl-alimask.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-alimask miniapp. + # +--- a/easel/miniapps/esl-alimerge.itest.pl ++++ b/easel/miniapps/esl-alimerge.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-alimerge miniapp. + # +--- a/easel/miniapps/esl-alistat.itest.pl ++++ b/easel/miniapps/esl-alistat.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-alistat miniapp. + # +--- a/easel/miniapps/esl-compalign.itest.pl ++++ b/easel/miniapps/esl-compalign.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-compalign miniapp. + # +--- a/easel/miniapps/esl-construct.itest.pl ++++ b/easel/miniapps/esl-construct.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-construct miniapp. + # +--- a/easel/miniapps/esl-mask.itest.pl ++++ b/easel/miniapps/esl-mask.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-mask miniapp. + # +--- a/easel/miniapps/esl-seqrange.itest.pl ++++ b/easel/miniapps/esl-seqrange.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-seqrange miniapp. + # +--- a/easel/miniapps/esl-shuffle.itest.pl ++++ b/easel/miniapps/esl-shuffle.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-shuffle miniapp + # +--- a/easel/miniapps/esl-ssdraw.itest.pl ++++ b/easel/miniapps/esl-ssdraw.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-ssdraw miniapp. + # +--- a/easel/testsuite/coverage_report.pl ++++ b/easel/testsuite/coverage_report.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Measures testsuite coverage (as percentage of source lines), + # using gcov. +--- a/easel/testsuite/driver_report.pl ++++ b/easel/testsuite/driver_report.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Make sure that all drivers compile. + # (Eventually, we should also make sure they run! But that +--- a/easel/testsuite/i1-degen-residues.pl ++++ b/easel/testsuite/i1-degen-residues.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integration tests of reading all valid protein sequence residue characters. + # +--- a/easel/testsuite/i2-ncbi-indices.pl ++++ b/easel/testsuite/i2-ncbi-indices.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Testing that we can read FASTA files, even if they have NCBI + # formatted BLAST databases in the same directory. +--- a/easel/testsuite/i3-blank-gf.pl ++++ b/easel/testsuite/i3-blank-gf.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #e5: blank text line following #=GF <tag> handled improperly. + # +--- a/easel/testsuite/valgrind_report.pl ++++ b/easel/testsuite/valgrind_report.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Run the testsuite under Valgrind, to check for memory leakage. + # +--- a/profmark/pmark-master.pl ++++ b/profmark/pmark-master.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # The top level script that runs a pmark benchmark. + # +--- a/profmark/rocplot.pl ++++ b/profmark/rocplot.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + $nsearches = 2809; + +--- a/src/hmmpress.itest.pl ++++ b/src/hmmpress.itest.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of hmmpress + # +--- a/testsuite/i10-duplicate-names.pl ++++ b/testsuite/i10-duplicate-names.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Check that we can deal with profiles and sequences that contain + # duplicate names, both as queries and targets. +--- a/testsuite/i11-hmmalign-mapali.pl ++++ b/testsuite/i11-hmmalign-mapali.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Another test of the hmmalign --mapali option, after Elena reports + # bug #h73 in bad interaction of checksum calculation and marking +--- a/testsuite/i12-delete-corruption.pl ++++ b/testsuite/i12-delete-corruption.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #h77: hmmalign corrupts column preceding an all-delete column + # +--- a/testsuite/i13-msa-integrity.pl ++++ b/testsuite/i13-msa-integrity.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Look for any problems in hmmalign that corrupt the input sequences. + # +--- a/testsuite/i14-hmmemit-consensus.pl ++++ b/testsuite/i14-hmmemit-consensus.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Tests hmmemit -c and hmmemit -C consensus-generating options. + # +--- a/testsuite/i15-hmmconvert.pl ++++ b/testsuite/i15-hmmconvert.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #h80: hmmconvert can't read H2 Nucleic files + # +--- a/testsuite/i16-build-allins.pl ++++ b/testsuite/i16-build-allins.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq + # +--- a/testsuite/i17-stdin.pl ++++ b/testsuite/i17-stdin.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test that programs accept and reject argument of '-' (for reading + # data from stdin, rather than from files) as they're supposed to. +--- a/testsuite/i18-nhmmer-generic.pl ++++ b/testsuite/i18-nhmmer-generic.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test of hmmbuild/nhmmer as used to build a DNA model, then query a + # a database of long (1MB). +--- a/testsuite/i19-hmmpgmd-ga.pl ++++ b/testsuite/i19-hmmpgmd-ga.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test that hmmpgmd is correctly applying bit score thresholds; + # in this case, the --cut_ga threshold, using an example that +--- a/testsuite/i20-fmindex-core.pl ++++ b/testsuite/i20-fmindex-core.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch + # +--- a/testsuite/i5-hmmbuild-naming.pl ++++ b/testsuite/i5-hmmbuild-naming.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test that HMM naming in hmmbuild works as advertised. + # Written to test for #h50. +--- a/testsuite/i6-hmmalign-mapali.pl ++++ b/testsuite/i6-hmmalign-mapali.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test the hmmalign --mapali option. + # +--- a/testsuite/i7-hmmbuild-fragments.pl ++++ b/testsuite/i7-hmmbuild-fragments.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test the ability of hmmbuild to deal with crappy alignments + # of lots of sequence fragments. +--- a/testsuite/i8-nonresidues.pl ++++ b/testsuite/i8-nonresidues.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Regression test of handling a nonresidue '*' character. By design, + # '*' residues score 0 in insert states and N,C,J; and -inf in match +--- a/testsuite/i9-optional-annotation.pl ++++ b/testsuite/i9-optional-annotation.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Check that we can deal with HMMs with no optional annotation, in either + # hmmscan or hmmsearch mode. +--- a/testsuite/test-make.pl ++++ b/testsuite/test-make.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Usage: test-make.pl <builddir> <srcdir> <tmppfx> + # diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild new file mode 100644 index 000000000000..cd0e1d732b8b --- /dev/null +++ b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +LICENSE="GPL-2" +HOMEPAGE="http://hmmer.org/" +SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" + +SLOT="2" +IUSE="altivec test threads" +KEYWORDS="~amd64 ~x86" + +DEPEND="test? ( dev-lang/perl )" +RDEPEND="" + +PATCHES=( + "${FILESDIR}/${P}-fix-perl-shebangs.patch" + "${FILESDIR}/${P}-fix-build-system-destdir.patch" +) + +src_configure() { + # prevent stray environmental variable + # from causing issues in the test phase + unset TMPDIR + + econf \ + --enable-lfs \ + $(use_enable altivec) \ + $(use_enable threads) +} + +src_install() { + default + + newlib.a src/libhmmer.a libhmmer2.a + insinto /usr/include/hmmer2 + doins src/*.h + + dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate} + dolib.a squid/libsquid.a + insinto /usr/include/hmmer2 + doins squid/*.h + + dodoc NOTES Userguide.pdf + newdoc 00README README + + # rename files due to collisions with hmmer-3 + # in order to make SLOTing possible + local i + + # first rename man pages... + pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die + for i in hmm*.1; do + mv ${i%.1}{,2}.1 || die + done + popd >/dev/null || die + + # ... then rename binaries + pushd "${ED%/}"/usr/bin/ >/dev/null || die + for i in hmm*; do + mv ${i}{,2} || die + done + popd >/dev/null || die +} + +pkg_postinst() { + elog "All ${P} binaries have been renamed, in order" + elog "to avoid collisions with hmmer-3. For instance" + elog + elog " hmmalign -> hmmalign2" + elog +} diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild new file mode 100644 index 000000000000..f94fcca8c295 --- /dev/null +++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PV="${PV/_beta/b}" + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +HOMEPAGE="http://hmmer.org/" +SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND=" + mpi? ( virtual/mpi ) + gsl? ( sci-libs/gsl:= )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +S="${WORKDIR}/${PN}-${MY_PV}" +PATCHES=( + "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch" + "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch" +) + +src_configure() { + # make build verbose, bug 429308 + export V=1 + + econf \ + --disable-pic \ + $(use_enable altivec vmx) \ + $(use_enable cpu_flags_x86_sse sse) \ + $(use_enable mpi) \ + $(use_enable threads) \ + $(use_with gsl) +} + +src_install() { + default + dodoc Userguide.pdf + + insinto /usr/share/${PN} + doins -r tutorial +} diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-biology/hmmer/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git 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a/sci-biology/iedera/iedera-1.04.ebuild b/sci-biology/iedera/iedera-1.04.ebuild new file mode 100644 index 000000000000..6be6fa802c94 --- /dev/null +++ b/sci-biology/iedera/iedera-1.04.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="2" + +DESCRIPTION="A subset seed design tool for DNA sequence alignment" +HOMEPAGE="http://bioinfo.lifl.fr/yass/iedera.php" +SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +src_install() { + einstall || die + dodoc AUTHORS README NEWS +} diff --git a/sci-biology/iedera/iedera-1.05-r1.ebuild b/sci-biology/iedera/iedera-1.05-r1.ebuild new file mode 100644 index 000000000000..115b5495f617 --- /dev/null +++ b/sci-biology/iedera/iedera-1.05-r1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="A subset seed design tool for DNA sequence alignment" +HOMEPAGE="http://bioinfo.lifl.fr/yass/iedera.php" +SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +PATCHES=( + "${FILESDIR}/${P}-fix-buildsystem.patch" +) + +src_prepare() { + mv configure.{in,ac} || die + default + eautoreconf +} diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/iedera/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest new file mode 100644 index 000000000000..d97cb531ca8b --- /dev/null +++ b/sci-biology/infernal/Manifest @@ -0,0 +1,10 @@ +AUX infernal-1.0.2-ldflags.patch 444 SHA256 db5d7d514d949dbe6f9e47961cc3e3e57898d6292fc6eb3675d69705737cecad SHA512 95f953bbf57a78f40df51bbfdab62e715905aa2bc57d4ca75e380c81d34c88d0177e6fe51933c908bf6e6f513b8c38ffeeb7c8f1802773c7c9773a36388b81d0 WHIRLPOOL 6c78e220702819ffe4ea25210a9b57052a37a24bed626cbc9970108358e76c0a5e3430ae44fcc92df78e3d8483f015e018f17928c999a359e3b4f8122596e5b0 +AUX infernal-1.0.2-overflows.patch 540 SHA256 692f1fecbb8e210e8b958d3a50584b4073ec129b6647da83f282e06949cb66ab SHA512 c8bafb2c10d09cae24f882d5238b6ae974669d59e0ee583bcedb13e81c88ea9859c1f78343d5be91a5cca05a3dc07ffe6436b33e201a46baf349795da5eec906 WHIRLPOOL ab0dd02643040650a40b717ec9f597c664bff9735e5ddc51a567dc9f4fc26a192f09212ee9ac0e10ade1061391517017416dde59dc4ccfef7d5876803dd6e739 +AUX infernal-1.0.2-parallel-build.patch 659 SHA256 79e8142c0970c7de12ebf2264b9ae1973dc9d1e76d672d0ffc2790a5aa95096b SHA512 d67271d858f60a5378d61892cd5c354ac95234620437621f3bf770e8829fa866a451ee031f530f502385044d7622f0fe88827614e95ab35ac6cbf8384d21e9c5 WHIRLPOOL 1513e00ecb5884ea3f1729f60862b3c3ee88b7686f331b8c2b00f078eb8ab5e2592510c7eee344516a559fcdaa8dd88ced11a212a15dee5806bb0361b1539722 +AUX infernal-1.0.2-perl-5.16-2.patch 4206 SHA256 db663878a8d139f1832ddbec54131c518cdbac1fa8d298e80cee529fb3eddd0f SHA512 9784f31c18f6c53b15c0454d3a41db27c3f433ac3d3030bc113e9f9e8194fb51109de5055d038a3c639b1c4142d6fd0010825df484a857c9f072f43d8cadcb44 WHIRLPOOL d8ce80893fe2abeb537daa0a759a432649f677d9cc9f77ff597b4a1bfb8d90b45ca4bae0043cd0fb889f6a14b0caa90d3d7cec9516f53d24e6b441fbfeb4dfe3 +AUX infernal-1.0.2-respect-DESTDIR.patch 396 SHA256 179a5e9fdb5f298cbab69f9dcbf3b97df7242702268e433e7bfeadcdee16379e SHA512 6847c87e45a34a68d179fbf8c9965af502cc9e52aa1f5ed800332dfb52e97ca3f2cb87a7dc4c3adb2d85f63567f15b084a50c7139f5ab03b0cf2b0711d023ec4 WHIRLPOOL 36981fcb327727c24364bc73ad3f80dc03628996c6c115677f676e02b1704d970329c3f87b812300d1897975373996ef54c3c4da343c2884fa29bdd8e880196f +DIST infernal-1.0.2.tar.gz 15205421 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af WHIRLPOOL c4fa3326eb1b36252ce41ca1aeca68bed4373061ca6bc2bfc0af62c0805bfa1747272fbf223b8d47194853ae5cbe7af11d47493c258264503ea6aa7b142a6b60 +EBUILD infernal-1.0.2-r1.ebuild 924 SHA256 db7e48034d9bca2ca4f0a385eb4451ed06d15029c45c9c76b4774f3b38869f3e SHA512 816308be6a7e57e30f7c22e0c37662cde9b234501e324889e7e21e4d0e779cc6bb113490f10ce1aba3aeff46bdf9668442878e3cea4d5ad171beeb0e9fe6832c WHIRLPOOL 51a7a1e7d6f615f2fd283ef8471181791b342b7dc7ef62d2093ec87ed06ae41f7f79a6b87a2dc47a416a02a8039a4d744d405205e2fe8b05fa7c1116969b8409 +MISC ChangeLog 2606 SHA256 479570cc326272ca6f0a2d16121de71e902d5e838def774c132b6dd6216ffe69 SHA512 c20696de2b14dc6720ccf55229941b69dc295c848b9236d902694e43425aed06389a90f3ce82e0bda9868028b49bf39cf847fe35089cb9d043e04340ce86cdde WHIRLPOOL 0340e76d90c707d2cc187e263cb6d5dde99d0724566a48c4188ad96b10d940858ef8a69d0d88a0884e55fc68f7ca126054a29c1bffd7c4620e469973b54e7e9d +MISC ChangeLog-2015 2575 SHA256 98f684e2671e5dcef3a9572874849d0bf01b8794e7ada1611c491816d8b8ef40 SHA512 371c177a61a11365b50244977c04f1d19cd3ae77425b11f29e39cb9e6ecc5a389cd4fcd0e24bf7fc9086874a03b64208ddac40c2d4ecb893296218a490ecc0ae WHIRLPOOL 3e6552a94f52d170421f1bce77fca59259cca376c1043f10e47c3274ba16089fbff2261817b88773d284b0ca0cd2d51e5078a7b43e973e6712197ab546c93a27 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch new file mode 100644 index 000000000000..f688dce152ed --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch @@ -0,0 +1,15 @@ +Respect LDFLAGS + +http://bugs.gentoo.org/show_bug.cgi?id=338177 + +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -86,7 +86,7 @@ + all: $(PROGS) + + $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} +- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) + + + ################################################################# diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch new file mode 100644 index 000000000000..67190c4c1d42 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch @@ -0,0 +1,15 @@ +Fix buffer overflow + +http://bugs.gentoo.org/show_bug.cgi?id=338179 + +--- a/easel/esl_getopts.c ++++ b/easel/esl_getopts.c +@@ -1270,7 +1270,7 @@ + "Arg looks like option? Use %.24s%.24s if you really mean it.", + g->opt[opti].name, *ret_optarg); + } else +- ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name); ++ ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name); + + g->optstring = NULL; /* An optchar that takes an arg must terminate an optstring. */ + } diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch new file mode 100644 index 000000000000..67ffa6fda7f6 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch @@ -0,0 +1,31 @@ +Fix parallel build + +http://bugs.gentoo.org/show_bug.cgi?id=311919 + +--- a/Makefile.in ++++ b/Makefile.in +@@ -82,9 +82,10 @@ + all: core + + core: +- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) +- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) +- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ $(MAKE) -C easel ++ $(MAKE) -C src ++ $(MAKE) -C src module ++ $(MAKE) -C testsuite + + #.PHONY: $(RIGFILTERS) + #$(RIGFILTERS): core +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -132,7 +132,7 @@ + esl_wuss.o + + all: libeasel.a +- (cd miniapps; make) ++ $(MAKE) -C miniapps + + .c.o: + ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< diff --git a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch new file mode 100644 index 000000000000..c96dcae7b296 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch @@ -0,0 +1,147 @@ + benchmarks/cmsearch-rmark/sre.pl | 4 +--- + easel/devkit/autodoc | 4 ++-- + easel/devkit/esl-dependencies | 4 ++-- + easel/devkit/sqc | 7 +++---- + easel/testsuite/coverage_report.pl | 4 ++-- + easel/testsuite/driver_report.pl | 4 ++-- + easel/testsuite/valgrind_report.pl | 4 ++-- + 7 files changed, 14 insertions(+), 17 deletions(-) + +diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl +index 9136717..e4df233 100644 +--- a/benchmarks/cmsearch-rmark/sre.pl ++++ b/benchmarks/cmsearch-rmark/sre.pl +@@ -6,8 +6,6 @@ + + package SRE_perlstuff; + +-require "importenv.pl"; +- + # Function: tempname + # + # Returns a unique temporary filename. +@@ -26,7 +24,7 @@ require "importenv.pl"; + # + sub main'tempname { + local ($dir, $name); +- if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";} + + foreach $suffix ("aa".."zz") { + $name = "$dir/sre$suffix$$"; +diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc +old mode 100755 +new mode 100644 +index 045ce36..22268f6 +--- a/easel/devkit/autodoc ++++ b/easel/devkit/autodoc +@@ -49,8 +49,8 @@ + # + # SRE, Tue Nov 30 19:43:47 2004 + +-require "getopts.pl"; +-&Getopts('n:t'); ++use Getopt::Std; ++getopts('n:t'); + $cfile = shift; + + if ($opt_t) { $show_api_table = 1; } +diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies +old mode 100755 +new mode 100644 +index a4dc126..b61fa7a +--- a/easel/devkit/esl-dependencies ++++ b/easel/devkit/esl-dependencies +@@ -13,8 +13,8 @@ + # SRE, Mon Jun 11 11:15:31 2007 + # SVN $Id$ + +-require "getopts.pl" +-&Getopts('1afr'); ++use Getopt::Std; ++getopts('1afr'); + + if ($opt_1) { $show_summary_table = 1; } + if ($opt_a) { $list_augfiles = 1; } +diff --git a/easel/devkit/sqc b/easel/devkit/sqc +old mode 100755 +new mode 100644 +index 81d03de..6201d3d +--- a/easel/devkit/sqc ++++ b/easel/devkit/sqc +@@ -176,12 +176,11 @@ + # SRE, Tue Aug 6 11:16:39 2002 + # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ + +-require "getopts.pl"; +-require "importenv.pl"; ++use Getopt::Std; + + # Parse our command line + # +-&Getopts('mp:r:v'); ++getopts('mp:r:v'); + if ($opt_m) { $do_memtest = 1; } + if ($opt_p) { push @prepdirs, $opt_p; } + if ($opt_r) { push @olddirs, $opt_r; } +@@ -510,7 +509,7 @@ check_ccmalloc_status + # + sub tempname { + my ($dir, $name, $suffix); +- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} + + foreach $suffix ("aa".."zz") { + $name = "$dir"."esltmp".$suffix.$$; +diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl +old mode 100755 +new mode 100644 +index 9c77791..024ed34 +--- a/easel/testsuite/coverage_report.pl ++++ b/easel/testsuite/coverage_report.pl +@@ -16,9 +16,9 @@ + # + # SRE, Thu Mar 1 19:22:57 2007 (Janelia) + # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ +-require "getopts.pl"; ++use Getopt::Std; + $have_sloccount = 1; +-&Getopts('cs'); ++getopts('cs'); + if ($opt_c) { $do_recompile = 1; } + if ($opt_s) { $have_sloccount = 0; } + +diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl +old mode 100755 +new mode 100644 +index d1b4a9a..db4378f +--- a/easel/testsuite/driver_report.pl ++++ b/easel/testsuite/driver_report.pl +@@ -19,8 +19,8 @@ + # SRE, Fri Mar 2 10:01:44 2007 (Janelia) + # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $ + +-require "getopts.pl"; +-&Getopts('c'); ++use Getopt::Std; ++getopts('c'); + if ($opt_c) { $do_recompile = 1; } + + if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } +diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl +old mode 100755 +new mode 100644 +index 186a392..07026a0 +--- a/easel/testsuite/valgrind_report.pl ++++ b/easel/testsuite/valgrind_report.pl +@@ -10,8 +10,8 @@ + # + # SRE, Fri Mar 2 08:37:48 2007 [Janelia] + # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ +-require "getopts.pl"; +-&Getopts('c'); ++use Getopt::Std; ++getopts('c'); + if ($opt_c) { $do_recompile = 1; } + + if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch new file mode 100644 index 000000000000..ea465e592ffa --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch @@ -0,0 +1,16 @@ +Build system does not respect DESTDIR by default. + +--- a/Makefile.in ++++ b/Makefile.in +@@ -203,9 +203,9 @@ + # "make install" installs the programs in BINDIR + # + install: +- mkdir -p ${BINDIR} ++ mkdir -p $(DESTDIR)${BINDIR} + for file in $(PROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ + done + # if test -d $(RIGFILTERS); then\ + # for file in $(RFPROGS); do\ diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild new file mode 100644 index 000000000000..e906c23024ff --- /dev/null +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Inference of RNA alignments" +HOMEPAGE="http://infernal.janelia.org/" +SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="mpi" +KEYWORDS="amd64 x86" + +RDEPEND="mpi? ( virtual/mpi )" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-parallel-build.patch + "${FILESDIR}"/${P}-overflows.patch + "${FILESDIR}"/${P}-perl-5.16-2.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-respect-DESTDIR.patch +) + +src_configure() { + econf $(use_enable mpi) +} + +src_install() { + DOCS=( 00README* Userguide.pdf documentation/release-notes ) + default + + pushd documentation/manpages >/dev/null || die + local i + for i in *.man; do + newman "${i}" "${i/.man/.1}" + done + popd >/dev/null || die + + insinto /usr/share/${PN} + doins -r benchmarks tutorial intro matrices +} diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/infernal/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/iqpnni/Manifest b/sci-biology/iqpnni/Manifest new file mode 100644 index 000000000000..871d1f2968bb --- /dev/null +++ b/sci-biology/iqpnni/Manifest @@ -0,0 +1,6 @@ +AUX iqpnni-3.3.2-cpp14.patch 1240 SHA256 47e6b0c1a1894685af11b29d864113cdeaf5e1a59f0c95d4daa005a1fce52a0f SHA512 64cba6133a64fdceff3c7c5ae7f2108e7115718609122fa4b647a6b48cd966774c20e2d9cbb4e8c4c1377de94bd57e07ef40b25692c4ee6d2282f8d4e04ddb78 WHIRLPOOL 56d1638476d2978bdeccfc411d408849c4b37c52611cfe24cbffa932e069fe51ddd558c12310738533567dc121a66ec1d1c8c6478e9b41770cfb2ba44b6dd148 +DIST iqpnni-3.3.2.tar.gz 646603 SHA256 e4ffc783c7444bfadd40c9d55e9fb0275fcf7dca80aa3217768c9bf63c28567f SHA512 6e603117b746956ad0c3b140968abf2b3b3065a18dc78cee4975f1d2e7971334fdde15e2e8d2fd7435b9490aaaffaf17a38f72a3897c951f493d866e21d94156 WHIRLPOOL f4319e93dd7c1e6700fed54f402aea50bceaf23eb352011105e2f9ea9f225772981b880acbb14a388eb1f9a415a8e0751374769131f634459daa415928ff08f1 +EBUILD iqpnni-3.3.2-r1.ebuild 582 SHA256 42ae0a9f82645a98ec76fdbc12bc3f2cb73ebe946a95dca9a6b86032bd7b4983 SHA512 ffaf3eb0c9384c52859bb598247850fa6b38dff9a1b75220b9596a10c5af1dd506edd66af0051cf7799003569665c7ec7c6dda02554e0757c57961988bf4afc2 WHIRLPOOL aba56c5dece718ee01f2efc325788adc6680b426ff614c9b627d9c5c13984975e7a855e14a7b8e51dd25ffd8a9c9884e7bf0f2d77bad8320bf3d061193f2764e +MISC ChangeLog 3276 SHA256 6def8052b068a89aa49f0cf1a7fd43e624554365fbf60f82bb0fada678710df8 SHA512 9aae3baa24a0f800f8f5260ea51348954ec1c828e780e9c0bcb8fe5b62238713b43255fbf0d5ce1a79cb61a0ccaee8824d8ff7c29694dfee598a5cef8c9f90c6 WHIRLPOOL c903401bdac610b2b15dd5054d07f6cc99e0139ecbe15d8d299bfce981edc0ae6b6040d700244c771d17d3a3796ec59582557d58dc41b1005547932d45c9d7f0 +MISC ChangeLog-2015 995 SHA256 b8d235bd4a74f81f84eff9fca80463a86132736a21d826a50e4e32e28b086918 SHA512 b73fc84b8ef72409cf961ec1a2cf905b59865c3882ee5d827e043412b3138cf3cb63d5558d0d355e286b139e80a6551ceac2d1d4c0fb10b6d268529526211f4f WHIRLPOOL 4bd0d5d67ef475f54ab50baf3d41857c6227bbb420f2a1816eab8a6eb6564e2462b606289724aa4b37ea6f68fb2cbb9552e99cc01402f0168f1b1685647d2b5b +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/iqpnni/files/iqpnni-3.3.2-cpp14.patch b/sci-biology/iqpnni/files/iqpnni-3.3.2-cpp14.patch new file mode 100644 index 000000000000..69a4aacb61b1 --- /dev/null +++ b/sci-biology/iqpnni/files/iqpnni-3.3.2-cpp14.patch @@ -0,0 +1,48 @@ +Fix problems with compilation in C++14 (GCC 6.x). Changes in iostream library +caused that comparison of istream to 0 or NULL is unavailable. +Gentoo bug: https://bugs.gentoo.org/show_bug.cgi?id=594332 + +--- a/src/interface.cpp ++++ b/src/interface.cpp +@@ -1340,7 +1340,7 @@ + + + int isExistedFile_ = 1; +- if (existedFile_ == 0) ++ if (!existedFile_) + isExistedFile_ = 0; + + existedFile_.close (); +--- a/src/iqp.cpp ++++ b/src/iqp.cpp +@@ -508,7 +508,7 @@ + if (in_pam.tree_file != NULL) {
+ std::ifstream userTreeFile_;
+ userTreeFile_.open (in_pam.tree_file);
+- if (userTreeFile_ != 0) {
++ if (userTreeFile_) {
+ initialTree_.readFile (in_pam.tree_file);
+ initialTree_.createUrTree ();
+ hasInitTree = true;
+--- a/src/main.cpp ++++ b/src/main.cpp +@@ -118,7 +118,7 @@ +
+ ifstream in;
+ in.open (boottree_file_name.c_str());
+- if (in == 0)
++ if (!in)
+ Utl::announceError ("Cannot open the user tree file ...");
+
+ int num_tree = 0;
+--- a/src/usertree.cpp ++++ b/src/usertree.cpp +@@ -94,7 +94,7 @@ + void UserTree::readFile (const char *userTreeFile) {
+ ifstream in;
+ in.open (userTreeFile);
+- if (in == 0)
++ if (!in)
+ Utl::announceError ("Cannot open the user tree file ...");
+
+ readFile(in);
diff --git a/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild new file mode 100644 index 000000000000..1edeeada187b --- /dev/null +++ b/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Important Quartet Puzzling and NNI Operation" +HOMEPAGE="http://www.cibiv.at/software/iqpnni/" +SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc" + +DEPEND="" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-cpp14.patch" # bug #594332 +) + +src_install() { + dobin src/iqpnni + + if use doc ; then + HTML_DOCS+=( manual/iqpnni-manual.html ) + dodoc manual/iqpnni-manual.pdf + fi + einstalldocs +} diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/iqpnni/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest new file mode 100644 index 000000000000..94722170730d --- /dev/null +++ b/sci-biology/kalign/Manifest @@ -0,0 +1,5 @@ +DIST kalign_2.03.orig.tar.gz 114022 SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0 SHA512 d60152bd7124f77ea972ea7dac19f47eb731646a12ecafbee8a99335c20a36fb3ce2bdc633b346e4da1016d8e56a0f297f9b33c9b6285197946f404dbc390b0a WHIRLPOOL 1793aed6e0c56a009f34d65a7dd36e0765de8bcb8fdd92590de677470f72b198bcc6afb0ceefce8246c38e7664a2ddd5ff446f585d782d8005c9ad8a8a79c13c +EBUILD kalign-2.03-r2.ebuild 601 SHA256 4a6fc67a975fe2b4c7afd07f540bf6828c2e5bafcc7f5761ed2c081ba1ef7225 SHA512 f19df61247a35a5a03164ad1a01968a078be043e53f53ff62ea35ba20787d84067fb4cd9212a9294a26270f95c7702ffdf571691df0311856f1de1973d6012ff WHIRLPOOL 27628257fc129db0fdfd2cf7c677b8068753ed2e8d5e74ba15cc32312cb046b8d747995769fb010f11a7b47049f488195a5d211e74278f755b29996b8a65df8a +MISC ChangeLog 2479 SHA256 cc8f03a314b443f4999c827685ee5cacb008161e0b167321ac4924981c52abc8 SHA512 b2f9909ab00f82b23d0a192f145219e6f9d404a6cb1e1aa2a4a911eb07af0749344a896f50d2f2c2bffe572c791905866500a7b4ac3f5a5e4b4a92a8918d95f3 WHIRLPOOL dd053787258b1b3b4cdc8e7e58705c9bd5a7c6f7d29e4d43a65ac38ac3e85cd1a3e8899e1615196ee6b4b188e0762d80fd2eafb4414f912f9b84fc7b4b47ac8d +MISC ChangeLog-2015 1215 SHA256 355eebb9633be71745c1a24d0f9efd43f28c84b1e1b2829019b5ace593fbdee0 SHA512 7b76e54de90eb5b58d194f7d8b72b1e51e79eba8bc216e4e8f251df2ce32b542bbca3a970b9fa737d0e6378b1f04644db320fdf2f0bf735a634c99625438c930 WHIRLPOOL ee820166c502ae50897c738872118b2e0f53e4c05b03111db0b067a2c4cca7134b1ed94deb253283992299b76342bc5ff7e68bda61b1f9102632eefd01f2d2bc +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/kalign/kalign-2.03-r2.ebuild b/sci-biology/kalign/kalign-2.03-r2.ebuild new file mode 100644 index 000000000000..53b4490bef71 --- /dev/null +++ b/sci-biology/kalign/kalign-2.03-r2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Global and progressive multiple sequence alignment" +HOMEPAGE="http://msa.cgb.ki.se/" +SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S=${WORKDIR}/${PN} + +src_prepare() { + default + sed \ + -e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \ + -i Makefile.in || die +} + +src_compile() { + emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" +} + +src_install() { + dobin ${PN} + einstalldocs +} diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/kalign/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest new file mode 100644 index 000000000000..db4846150a7a --- /dev/null +++ b/sci-biology/lagan/Manifest @@ -0,0 +1,9 @@ +AUX lagan-2.0-fix-c++14.patch 13525 SHA256 d7c7a98101911c15cdbea1b4f1ce3ace93299151e9665a7c8b0f1148427ed3b9 SHA512 f62b523cf9692a1394276ac674ccf7ce9a0070c646c95d1f20b8e0ace61afffd04aae3a098511bb106ab62089e70bebfae6ba25aaffcccbbe7f8397a30c2900a WHIRLPOOL 2332dd6fbf1831c74b1e8e863bbaa7649e2ea70872d9890cfa0cec0ad4f64c16dd0791eacf3bb52d17981920de07234c8642e85fe1df3a5e5de48f27fe719ff5 +AUX lagan-2.0-flags.patch 5848 SHA256 258c3fdcf1eddb4f2282cb45d6113d3e056f42c87442cceef24af463d0e9cf4f SHA512 63917ed217c44cade1c87dd6498cb7f6180c30eaba3875fa77f7e73b894aadab1469aca87650d1017a44fcac548552c3bdfcaff29b24023d23c7424079ad91cf WHIRLPOOL 895cc7aedc3c3504acc94796002abe8d6be36e1ab799e272d9034ed19cdb1f37f8d3481b925c63797d32ff5fbb343b7b07151fe4dbdf42a10de9632cf675b498 +AUX lagan-2.0-gcc4.3.patch 821 SHA256 e0575359288e7de97d35a7cce7b92c5619d2f75026beefc9139042280aa20a22 SHA512 91b56b0cfc27f799fed164a8a32b4840ea2e7f7796d334b2bce8bd27bc2fb96b4cdb0912c737c874f767a16ffcdd4e4623a0f80a35082aa4289882d1502cc0df WHIRLPOOL dd6cbe280e3fe69c3e1b3c1cf706cafb3521be394575481eb3595c578f2df069f8717195213abfcb6ce1f3576a8943d7f9823112052b169c24f8d03bc8e6807b +AUX lagan-2.0-qa-implicit-declarations.patch 2371 SHA256 2fdaf4c16206300f89d447d05f06a66a77620f6aa1a402f5e2a08e28a97a0b0e SHA512 eec54cec02a5c8c875a4d64238276f116baa8f3d780573ca5143621ca62a1e96ba4045ae37d45321fc040b78216607d787c2c6c909a8264f17f99a0e07295bf5 WHIRLPOOL 63dd394b1aa076c1b0a46a9afa96033bab468370dbb7888de351168015feb0ba21124a0fef571de5b82eed3d525aa443f2e647dafda686f7faa0c9e41f180bab +DIST lagan20.tar.gz 589115 SHA256 a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe SHA512 f77217ab534df33834a725eb6e1b716f7bbffa98768a42c2294a6ab62404192e560bb05ffd41e4cdccb5b96ef9efceb8ecdc06472bbc6a301e1d11572ba29b98 WHIRLPOOL 3400b8da7dae1431f18f8aeada17161f48d8e548f79d312cf153dc9b360f1bb7103fc6ff799d798c46898d6f62928a241146e09871f1b40e93d10118ca71a553 +EBUILD lagan-2.0-r3.ebuild 1659 SHA256 8ae3f84d205c9064b40dc32a709e470457f74774d21e6ab477a659711835b97f SHA512 b5efe429851ae0a3676a6e63017ebabdcae169667d091b2e69c0c2daa401f34e0ff3b789f8bacd78376befc466bb20de8f0d80bae63c332a6c412f01794f457b WHIRLPOOL ad8741e76441265976d75e1b8a0b3c3c204b60a437cd6dfb8db65b08dcf54dd9b485142b0b44072b5b258ecbe2ea256b79a198563615d0b0212b425349aac1f7 +MISC ChangeLog 3075 SHA256 4ae47c42c216508fc7efe046bfcc256d60a2130fad10930f4fba7f9cd5445647 SHA512 ec9097994dd597f31f0c7998a3b69370d5870729c2a84366206ec2008e46b265ec3254b829bd3c7b6cc3155d899e938664bbb34dd6d95625db2ef2ca6249fbca WHIRLPOOL b3a696f08a9306ed58349b112d6764eaa4ffa0fd7016a71960670230c5d17e4ac1c3069e8f3f8669dd5920fc635f743809647a1d823017de9308218060c2b3d2 +MISC ChangeLog-2015 990 SHA256 f6053e432b2071a1b37fd0d1f99bcff716693104eb3b0194e66bdf751c786dcd SHA512 8c0583b884882009dc1c431dd44cd93ac4b8c3e8a8623255027ececa12ace992141db5ac75cd4562504131c85c0f471b208faf8a36508b92028280bd41447c31 WHIRLPOOL aacfaa6f338065282b1c37ac3dfbc67ba4a60086bb2e2e74699a63877d07c75f68daa8b32770ef114abc3c516c0fdfdd8b5fb3d615f3ff15eda718669b88c7f2 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch new file mode 100644 index 000000000000..9865f2756c5a --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch @@ -0,0 +1,473 @@ +Fix building with C++14, which errors out due to namespace collisions with std::end +in C++14 mode, due to crappy 'using namespace std' declared everywhere. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594148 + +--- a/src/ancseq.cpp ++++ b/src/ancseq.cpp +@@ -30,7 +30,6 @@ + #include <stdlib.h> + #include <stdio.h> + +-using namespace std; + + #include "util.cpp" + #include "faindex.cpp" +--- a/src/ancseqrest.cpp ++++ b/src/ancseqrest.cpp +@@ -31,7 +31,6 @@ + #include <stdlib.h> + #include <stdio.h> + +-using namespace std; + + #define fastaRowLength 50 + typedef char* pchar; +--- a/src/cutmfa.cpp ++++ b/src/cutmfa.cpp +@@ -45,7 +45,6 @@ + #include <stdlib.h> + #include <stdio.h> + +-using namespace std; + + // TODO refactor in classes and normal make project + +--- a/src/glocal/glocal.cpp ++++ b/src/glocal/glocal.cpp +@@ -7,9 +7,9 @@ + } + + //vectors that would be needed globally +-vector<Fragment> fragments; +-vector<Point>startPoints; +-vector<Point>endPoints; ++std::vector<Fragment> fragments; ++std::vector<Point>startPoints; ++std::vector<Point>endPoints; + long long int numFragments; + InterPoint inter; + +@@ -19,7 +19,7 @@ + RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + +-vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; ++std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + + Name allNames; + +--- a/src/glocal/io.cpp ++++ b/src/glocal/io.cpp +@@ -3,9 +3,9 @@ + #include<io.h> + #include<algorithm> + +-extern vector <Fragment> fragments; +-extern vector <Point> startPoints; +-extern vector <Point> endPoints; ++extern std::vector <Fragment> fragments; ++extern std::vector <Point> startPoints; ++extern std::vector <Point> endPoints; + extern Name allNames; + + bool PointCompare(const Point &f1, const Point &f2) { +@@ -223,8 +223,8 @@ + startPoints.push_back(startPoint); + endPoints.push_back(endPoint); + } +- sort(startPoints.begin(), startPoints.end(), PointCompare); +- sort(endPoints.begin(), endPoints.end(), PointCompare); ++ std::sort(startPoints.begin(), startPoints.end(), PointCompare); ++ std::sort(endPoints.begin(), endPoints.end(), PointCompare); + } + + +--- a/src/glocal/leftinfluence.cpp ++++ b/src/glocal/leftinfluence.cpp +@@ -154,8 +154,8 @@ + + if (second->score == -1) { return TRUE; } + +- dummy.seq1Start = max(first->seq1End, second->seq1End) + 2; +- dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; ++ dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2; ++ dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1; + + if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) { + dummy.nameIter = first->nameIter; +@@ -444,7 +444,7 @@ + temp.seq1 = col - diag; + temp.seq2 = col; + +- pair<Point,LI*> pairp(temp, LeftInfluence); ++ std::pair<Point,LI*> pairp(temp, LeftInfluence); + tempinter = inter.insert(pairp); + + colInter->second = tempinter; +--- a/src/glocal/leftinfluence.h ++++ b/src/glocal/leftinfluence.h +@@ -39,15 +39,15 @@ + + + +-typedef list<Fragment*> Owner; +-typedef map <long long int ,Owner::iterator,longlongCompare2> CBound; ++typedef std::list<Fragment*> Owner; ++typedef std::map <long long int ,Owner::iterator,longlongCompare2> CBound; + +-typedef multimap <Point ,struct LI *,paircomp> InterPoint; ++typedef std::multimap <Point ,struct LI *,paircomp> InterPoint; + +-typedef map <long long int ,InterPoint::iterator,longlongCompare2> CInter; +-typedef map <long long int,Owner::iterator,longlongCompare2> DBound; ++typedef std::map <long long int ,InterPoint::iterator,longlongCompare2> CInter; ++typedef std::map <long long int,Owner::iterator,longlongCompare2> DBound; + +-typedef map <long long int,InterPoint::iterator,longlongCompare2> DInter; ++typedef std::map <long long int,InterPoint::iterator,longlongCompare2> DInter; + + + +--- a/src/glocal/rightinfluence.h ++++ b/src/glocal/rightinfluence.h +@@ -17,7 +17,7 @@ + }; + + +-typedef map<const long long int , Fragment*,longlongCompare> Active; ++typedef std::map<const long long int , Fragment*,longlongCompare> Active; + + typedef struct RI { + //List of active regions +--- a/src/glocal/score.cpp ++++ b/src/glocal/score.cpp +@@ -4,7 +4,7 @@ + #include<rightinfluence.h> + #include<fstream> + +-extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; ++extern std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + + + float Score::getScore(Fragment *up, Fragment * down) { +@@ -36,7 +36,7 @@ + + + void initScoreFunctionPointers(char * scoreFileName) { +- ifstream SFP; ++ std::ifstream SFP; + char line[255]; + + SFP.open(scoreFileName); +--- a/src/glocal/structs.h ++++ b/src/glocal/structs.h +@@ -12,7 +12,6 @@ + #include <list> + #include <string.h> + +-using namespace std; + + #define RIGHT 0 + #define LEFT 1 +@@ -49,7 +48,7 @@ + }; + + +-typedef map<const char*,long long int ,ltstr> Name; ++typedef std::map<const char*,long long int ,ltstr> Name; + + + typedef struct Fragment { +--- a/src/lagan2mfa.cpp ++++ b/src/lagan2mfa.cpp +@@ -6,7 +6,6 @@ + #include <stdlib.h> + #include <stdio.h> + +-using namespace std; + + // TODO refactor in classes and normal make project + +--- a/src/makecons.cpp ++++ b/src/makecons.cpp +@@ -18,7 +18,6 @@ + #include <ctype.h> + #include <time.h> + +-using namespace std; + + #define fastaRowLength 50 + #define bufSize 2000 +--- a/src/utils/Glue.cpp ++++ b/src/utils/Glue.cpp +@@ -170,7 +170,7 @@ + } + + void printCoordinates (int seq, int begin, int end){ +- cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; ++ std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " "; + } + + int printRegion (int begin, int end){ +@@ -183,7 +183,7 @@ + score += rescoreRegion (seqs[i], seqs[j], begin, end); + } + } +- cout << score << endl; ++ std::cout << score << std::endl; + return score; + } + +@@ -223,7 +223,7 @@ + } + } + +- cout << "= score=" << score << endl; ++ std::cout << "= score=" << score << std::endl; + } + + int countLets (SafeVector<char> &data){ +@@ -355,7 +355,7 @@ + FILE* outfile; + + if (argc < 2 || argc > 3){ +- cerr << "Usage: Glue align.mfa \n" << endl; ++ std::cerr << "Usage: Glue align.mfa \n" << std::endl; + exit (1); + } + +@@ -375,7 +375,7 @@ + SafeVector<int> merged1label, merged2label; + int begin1 = 1, end1 = 1; + +- ifstream data (argv[1]); ++ std::ifstream data (argv[1]); + int alignNum = 0; + strand.push_back ('?'); // nothing for alignNum 0 + +@@ -452,7 +452,7 @@ + SafeVector<char> temp1 (begin1 - 1, 'N'); + SafeVector<char> temp2 (begin1 - 1, '-'); + +- for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++) ++ for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++) + temp2[i] = 'N'; + + merged1 = merge (temp1, merged1); +@@ -471,12 +471,12 @@ + if (isalpha(merged2[j])) pos2++; + + if (merged1label[j] == i){ +- min1 = min (min1, pos1); +- max1 = max (max1, pos1); ++ min1 = std::min (min1, pos1); ++ max1 = std::max (max1, pos1); + } + if (merged2label[j] == i){ +- min2 = min (min2, pos2); +- max2 = max (max2, pos2); ++ min2 = std::min (min2, pos2); ++ max2 = std::max (max2, pos2); + } + } + +@@ -489,6 +489,6 @@ + fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2); + } + +- printMFA (cout, merged1, string ("first"), 60); +- printMFA (cout, merged2, string ("second"), 60); ++ printMFA (std::cout, merged1, std::string ("first"), 60); ++ printMFA (std::cout, merged2, std::string ("second"), 60); + } +--- a/src/utils/MultiSequence.h ++++ b/src/utils/MultiSequence.h +@@ -12,7 +12,6 @@ + #include "Sequence.h" + #include "SafeVector.h" + +-using namespace std; + + class MultiSequence { + private: +@@ -54,10 +53,10 @@ + + // Read in all of the Sequences in an MFA file and append them to the + // existing MultiSequence object. +- void addRawFromMFA (const string& filename){ ++ void addRawFromMFA (const std::string& filename){ + + // open up file for reading +- ifstream infile (filename.c_str()); ++ std::ifstream infile (filename.c_str()); + + // check for error + assert (!infile.fail()); +@@ -75,7 +74,7 @@ + + // Read in all of the Sequences in an MFA file and append them to the + // existing MultiSequence object. +- void addRawFromMFA (ifstream &infile){ ++ void addRawFromMFA (std::ifstream &infile){ + + // check for error + assert (!infile.fail()); +@@ -89,7 +88,7 @@ + } + + // Writes sequences to outfile in XMFA format. +- void writeToXMFA (ostream &outfile, int numColumns) const { ++ void writeToXMFA (std::ostream &outfile, int numColumns) const { + for (int i = 0; i < (int) sequences.size(); ++i){ + sequences[i].writeToXMFA (outfile, numColumns); + } +--- a/src/utils/Output.h ++++ b/src/utils/Output.h +@@ -2,18 +2,18 @@ + #define OUTPUT_H + + // print reversed string in MFA format +-void printMFA (ostream &outfile, SafeVector<char> &data, string comment, int numColumns){ ++void printMFA (std::ostream &outfile, SafeVector<char> &data, std::string comment, int numColumns){ + + int charsWritten = 0; + +- outfile << ">" << comment << endl; ++ outfile << ">" << comment << std::endl; + for (int i = 0; i < (int) data.size(); i++){ + outfile << data[i]; + charsWritten++; +- if (charsWritten % numColumns == 0) outfile << endl; ++ if (charsWritten % numColumns == 0) outfile << std::endl; + } + +- if (charsWritten % numColumns != 0) outfile << endl; ++ if (charsWritten % numColumns != 0) outfile << std::endl; + } + + +--- a/src/utils/SafeVector.h ++++ b/src/utils/SafeVector.h +@@ -10,7 +10,6 @@ + #include <assert.h> + #include <vector> + +-using namespace std; + + // class derived from the STL std::vector + template<class TYPE> +@@ -19,9 +18,9 @@ + + // miscellaneous constructors + SafeVector () {} +- SafeVector (size_t size) : vector<TYPE>(size) {} +- SafeVector (size_t size, const TYPE &value) : vector<TYPE>(size, value) {} +- SafeVector (const SafeVector &source) : vector<TYPE>(source) {} ++ SafeVector (size_t size) : std::vector<TYPE>(size) {} ++ SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {} ++ SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {} + + #ifdef ENABLE_CHECKS + +--- a/src/utils/Sequence.h ++++ b/src/utils/Sequence.h +@@ -8,15 +8,14 @@ + #include <string> + #include "SafeVector.h" + +-using namespace std; + + class Sequence { + + private: + + // Read header of MFA/XMFA file. +- bool readHeader (ifstream &infile, bool &isXMFA){ +- string header; ++ bool readHeader (std::ifstream &infile, bool &isXMFA){ ++ std::string header; + + while (true){ + +@@ -24,7 +23,7 @@ + if (infile.fail() || infile.eof()) return false; + + // get new header line +- getline (infile, header); ++ std::getline (infile, header); + + // check that header line is not empty + if (header.length() != 0) break; +@@ -64,7 +63,7 @@ + int startCoord; // sequence position of first character + int endCoord; // sequence position of last character + char direction; // + or - +- string comment; // comments ++ std::string comment; // comments + + public: + +@@ -77,7 +76,7 @@ + } + + // Constructor. Reads in a sequence from the input file. +- Sequence (ifstream &infile){ ++ Sequence (std::ifstream &infile){ + + bool isXMFA = true; + +@@ -147,7 +146,7 @@ + } + + // Constructor. Gets sequence from array data. +- Sequence (SafeVector<char> data, string comment) : data(data), comment(comment) { ++ Sequence (SafeVector<char> data, std::string comment) : data(data), comment(comment) { + length = data.size() - 1; + id = 0; + startCoord = 1; +@@ -165,7 +164,7 @@ + return temp; + } + +- const string getComment () const { ++ const std::string getComment () const { + return comment; + } + +@@ -197,9 +196,9 @@ + const int getEndCoord () const { assert (isValid); return endCoord; } + + // Print XMFA header only. +- void writeXMFAHeader (ostream &outfile) const { ++ void writeXMFAHeader (std::ostream &outfile) const { + assert (isValid); +- outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; ++ outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl; + } + + // Return sequence ID. +@@ -209,20 +208,20 @@ + void setID (int id) { assert (isValid); this->id = id; } + + // Writes sequence to XMFA format. +- void writeToXMFA (ostream &outfile, int numColumns) const { ++ void writeToXMFA (std::ostream &outfile, int numColumns) const { + + assert (isValid); + + // print XMFA header +- outfile << ">" << comment << endl; ++ outfile << ">" << comment << std::endl; + // outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl; + + // print character data + for (int i = 1; i <= length; ++i){ + outfile << data[i]; +- if (i % numColumns == 0) outfile << endl; ++ if (i % numColumns == 0) outfile << std::endl; + } +- if (length % numColumns != 0) outfile << endl; ++ if (length % numColumns != 0) outfile << std::endl; + } + }; + diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-flags.patch new file mode 100644 index 000000000000..e324ef64c4c6 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-flags.patch @@ -0,0 +1,107 @@ +diff --git a/Makefile b/Makefile +index fbbbe79..a1d449b 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,5 @@ + all: +- (cd src; $(MAKE)) ++ $(MAKE) -C src + clean: + rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay + (cd src; $(MAKE) clean) +diff --git a/src/Makefile b/src/Makefile +index 7f6b6fd..dd6309b 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W + TRGT_DIR = .. + + all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay +- (cd glocal; $(MAKE)) ++ $(MAKE) -C glocal + clean: + rm -f *.o *~ utils/*~ mlagan.purify core + (cd glocal; $(MAKE) clean) + ../anchors: anchors.c skiplist.c +- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c + ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG + ../order: order.c diagmatrix.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c + ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../utils/bin2mf: utils/bin2mf.c +- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c + ../utils/bin2bl: utils/bin2bl.c +- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c + ../utils/cextract: utils/cextract.c +- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c + ../utils/cstat: utils/cstat.c +- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c + ../utils/contigorder: utils/contigorder.c +- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c + ../utils/getbounds: utils/getbounds.c +- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c + ../utils/getcontigpos: utils/getcontigpos.c +- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c + ../utils/getlength: utils/getlength.c +- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c + ../utils/getoverlap: utils/getoverlap.c +- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c + ../utils/rc: utils/rc.c +- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c + ../utils/seqmerge: utils/seqmerge.c +- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c + ../utils/scorealign: utils/scorealign.c +- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm + ../utils/scorecontigs: utils/scorecontigs.c +- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm + ../utils/fa2xfa: utils/fa2xfa.c +- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c + ../utils/overlay: utils/overlay.c +- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c + ../utils/Glue: utils/Glue.cpp +- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp + ../utils/dotplot: utils/dotplot.cpp +- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp +diff --git a/src/glocal/Makefile b/src/glocal/Makefile +index ce1421a..b82507f 100755 +--- a/src/glocal/Makefile ++++ b/src/glocal/Makefile +@@ -10,10 +10,10 @@ TRGT = glocal + OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o + + .cpp.o: +- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp ++ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp + + $(TRGT): $(OBJECTS) +- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) ++ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) + + clean : + rm -f *.o ./*~ *~ core diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch new file mode 100644 index 000000000000..a4b1d6808e2f --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch @@ -0,0 +1,23 @@ +diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp +--- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000 ++++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000 +@@ -2,7 +2,7 @@ + #include<score.h> + #include<leftinfluence.h> + #include<rightinfluence.h> +-#include<fstream.h> ++#include<fstream> + + extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + +diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp +--- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000 ++++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000 +@@ -1,6 +1,7 @@ + #include "MultiSequence.h" + #include "SafeVector.h" + #include "Output.h" ++#include <string.h> + #include <math.h> + #include <assert.h> + #include <fstream> diff --git a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch new file mode 100644 index 000000000000..4ba4ce49d770 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch @@ -0,0 +1,96 @@ +Fix QA warnings due to implicit declarations: +* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] +* temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? + +--- a/src/filebuffer.c ++++ b/src/filebuffer.c +@@ -3,6 +3,7 @@ + #include <string.h> + #include <stdio.h> + #include <assert.h> ++#include <ctype.h> + + #ifdef CHAOS__FLAG + char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*"; +--- a/src/mlagan.c ++++ b/src/mlagan.c +@@ -934,6 +934,7 @@ + return k; + } + ++int printXMFAAlign(FILE* outfile, align* myalign); + + int main(int argc, char** argv) { + FileBuffer seqfile; +--- a/src/order.c ++++ b/src/order.c +@@ -398,6 +398,9 @@ + free(ends); + } + ++int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2); ++int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2); ++ + void doAlign(dmat* mydm, seq* seq1, seq* seq2) { + align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets); + // printf("into printing\n"); +--- a/src/prolagan.c ++++ b/src/prolagan.c +@@ -949,6 +949,7 @@ + return k; + } + ++int printXMFAAlign(FILE* outfile, align* myalign); + + int main(int argc, char** argv) { + FileBuffer seqfile; +--- a/src/utils/contigorder.c ++++ b/src/utils/contigorder.c +@@ -12,7 +12,7 @@ + int dummy, i; + + if (!(file = fopen (filename, "r"))){ +- fprintf (stderr, "contigorder: Error opening file: %s\n"); ++ fprintf (stderr, "contigorder: Error opening file: %s\n", filename); + exit (1); + } + +@@ -49,7 +49,7 @@ + } + + if (!(file = fopen (filename, "r"))){ +- fprintf (stderr, "contigorder: Error opening file: %s\n"); ++ fprintf (stderr, "contigorder: Error opening file: %s\n", filename); + exit (1); + } + +--- a/src/utils/cstat.c ++++ b/src/utils/cstat.c +@@ -3,6 +3,7 @@ + #include <string.h> + #include <math.h> + #include <assert.h> ++#include <ctype.h> + + #define MAX_SEQ 31 + #define MAX(a,b) ((a)>(b)?(a):(b)) +--- a/src/utils/overlay.c ++++ b/src/utils/overlay.c +@@ -2,6 +2,7 @@ + #include <stdio.h> + #include <assert.h> + #include <string.h> ++#include <ctype.h> + + #define MAX_SEQS 63 + #define MIN2(y,z) ((y)<(z))?(y):(z) +--- a/src/utils/scorecontigs.c ++++ b/src/utils/scorecontigs.c +@@ -3,6 +3,7 @@ + #include <string.h> + #include <math.h> + #include <assert.h> ++#include <ctype.h> + + #define MAX_SEQ 1024 + #define MAX(a,b) ((a)>(b)?(a):(b)) diff --git a/sci-biology/lagan/lagan-2.0-r3.ebuild b/sci-biology/lagan/lagan-2.0-r3.ebuild new file mode 100644 index 000000000000..e326331e09fb --- /dev/null +++ b/sci-biology/lagan/lagan-2.0-r3.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_P="lagan20" + +DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA" +HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" +SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}/${PN}-2.0-flags.patch" + "${FILESDIR}/${PN}-2.0-gcc4.3.patch" + "${FILESDIR}/${PN}-2.0-fix-c++14.patch" + "${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch" +) + +src_prepare() { + sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die + # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h + # where libc getline is erroneously used instead of own getline + sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die + + default +} + +src_compile() { + emake \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" +} + +src_install() { + newbin lagan.pl lagan + newbin slagan.pl slagan + dobin mlagan + rm -f lagan.pl slagan.pl utils/Utils.pm || die + + insinto /usr/$(get_libdir)/${PN}/lib + doins Utils.pm + + exeinto /usr/$(get_libdir)/${PN}/utils + doexe utils/* + + exeinto /usr/$(get_libdir)/${PN} + doexe *.pl anchors chaos glocal order prolagan + + insinto /usr/$(get_libdir)/${PN} + doins *.txt + + dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap + + echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die + doenvd 99${PN} + + dodoc Readmes/README.* +} diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/lagan/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest new file mode 100644 index 000000000000..ab42266146cf --- /dev/null +++ b/sci-biology/last/Manifest @@ -0,0 +1,9 @@ +AUX last-299-fix-build-system.patch 2021 SHA256 d963e2478ae16605d41fb152ad5680bbf7940ae114e583696790d512c4587a4e SHA512 42df26ce39dd8d263581f20aee0a3fbea0c849fcb5b1627554f9d0b3d3cea55a13b7f42fca9048611a50fdd9e784fa2b537a876b6ded411601c78b2e13e2e19c WHIRLPOOL 688375499b15d031fd55f68a8337e45418ced59bd374026950fd21e0bd6b6af1aa0d026306c591ef6d350de8219091434e13b1fd70aea054fa69c946b5f9711d +AUX last-299-portable-shebangs.patch 2762 SHA256 79c7de9eb995bd645ca0ef1273ea9ae75b2d4753e9c2ac0de520181e2e3d58f4 SHA512 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d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/last/files/last-299-fix-build-system.patch b/sci-biology/last/files/last-299-fix-build-system.patch new file mode 100644 index 000000000000..0a89cea60278 --- /dev/null +++ b/sci-biology/last/files/last-299-fix-build-system.patch @@ -0,0 +1,74 @@ +Make build system respect user flags + +--- a/makefile ++++ b/makefile +@@ -1,6 +1,5 @@ +-CXXFLAGS = -O3 + all: +- @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)" ++ $(MAKE) -C src + + prefix = /usr/local + exec_prefix = $(prefix) +@@ -10,15 +9,15 @@ + cp src/last?? scripts/*.?? $(bindir) + + clean: +- @cd src && $(MAKE) clean ++ $(MAKE) -C src clean + + html: +- @cd doc && $(MAKE) ++ $(MAKE) -C doc + + distdir = last-`hg id -n` + + dist: log html +- @cd src && $(MAKE) version.hh ++ $(MAKE) -C src version.hh + rsync -rC --exclude 'last??' doc examples makefile s* *.txt $(distdir) + zip -qrm $(distdir) $(distdir) + +--- a/src/makefile ++++ b/src/makefile +@@ -1,12 +1,9 @@ +-CXX = g++ +-CC = gcc +- +-CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ +--Wcast-align -Wno-long-long -ansi -pedantic ++last_CXXFLAGS = -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef \ ++-Wcast-align -Wno-long-long -pedantic + # -Wconversion + # -fomit-frame-pointer ? + +-CFLAGS = -Wall ++last_CFLAGS = -Wall + + DBSRC = Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc \ + SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc \ +@@ -49,17 +46,20 @@ + + all: lastdb lastal lastex + ++.cpp.o: ++ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) -c -o $@ $< ++ + lastdb: $(DBSRC) $(DBINC) makefile +- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC) ++ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC) + + lastal: $(ALSRC) $(ALINC) makefile $(OBJ) +- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ) ++ $(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ) + + lastex: $(EXSRC) $(EXINC) makefile +- $(CXX) -Igumbel_params $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC) ++ $(CXX) $(CPPFLAGS) -Igumbel_params $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC) + + $(OBJ): CA_code/*.c CA_code/*.h makefile +- $(CC) $(CPPFLAGS) $(CFLAGS) -c CA_code/lambda_calculator.c ++ $(CC) $(CPPFLAGS) $(last_CFLAGS) $(CFLAGS) -c -o $@ CA_code/lambda_calculator.c + + clean: + rm -f lastdb lastal lastex $(OBJ) diff --git a/sci-biology/last/files/last-299-portable-shebangs.patch b/sci-biology/last/files/last-299-portable-shebangs.patch new file mode 100644 index 000000000000..03ecbdcbde20 --- /dev/null +++ b/sci-biology/last/files/last-299-portable-shebangs.patch @@ -0,0 +1,99 @@ +Make shebangs portable and prefix friendly +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/scripts/last-dotplot.py ++++ b/scripts/last-dotplot.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Read pair-wise alignments in MAF or LAST tabular format: write an + # "Oxford grid", a.k.a. dotplot. +--- a/scripts/last-map-probs.py ++++ b/scripts/last-map-probs.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Copyright 2010, 2011, 2012 Martin C. Frith + +--- a/scripts/last-merge-batches.py ++++ b/scripts/last-merge-batches.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Copyright 2010, 2011 Martin C. Frith + +--- a/scripts/last-pair-probs.py ++++ b/scripts/last-pair-probs.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Copyright 2011, 2012, 2013 Martin C. Frith + +--- a/scripts/last-reduce-alignments.sh ++++ b/scripts/last-reduce-alignments.sh +@@ -1,4 +1,4 @@ +-#! /bin/sh ++#!/usr/bin/env sh + + # This script reads MAF-format alignments with lastal header + # information, removes "uninteresting" alignments, and writes the +--- a/scripts/last-remove-dominated.py ++++ b/scripts/last-remove-dominated.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Read MAF-format alignments, and write those are not "dominated" by + # any other one. X dominates Y if they overlap on the top sequence, +--- a/scripts/last-split-probs.py ++++ b/scripts/last-split-probs.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Copyright 2012 Martin C. Frith + +--- a/scripts/maf-convert.py ++++ b/scripts/maf-convert.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + # Copyright 2010, 2011 Martin C. Frith + # Read MAF-format alignments: write them in other formats. + # Seems to work with Python 2.x, x>=4 +--- a/scripts/maf-cull.py ++++ b/scripts/maf-cull.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Read MAF-format alignments. Write them, omitting alignments whose + # coordinates in the top-most sequence are contained in those of >= +--- a/scripts/maf-join.py ++++ b/scripts/maf-join.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Copyright 2009, 2010, 2011 Martin C. Frith + +--- a/scripts/maf-sort.sh ++++ b/scripts/maf-sort.sh +@@ -1,4 +1,4 @@ +-#! /bin/sh ++#!/usr/bin/env sh + + # Sort MAF-format alignments by sequence name, then strand, then start + # position, then end position, of the top sequence. Also, merge +--- a/scripts/maf-swap.py ++++ b/scripts/maf-swap.py +@@ -1,4 +1,4 @@ +-#! /usr/bin/env python ++#!/usr/bin/env python2 + + # Read MAF-format alignments, and write them, after moving the Nth + # sequence to the top in each alignment. diff --git a/sci-biology/last/last-230.ebuild b/sci-biology/last/last-230.ebuild new file mode 100644 index 000000000000..29134bb908df --- /dev/null +++ b/sci-biology/last/last-230.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Genome-scale comparison of biological sequences" +HOMEPAGE="http://last.cbrc.jp/" +SRC_URI="http://last.cbrc.jp/archive/${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_prepare() { + sed \ + -e 's:-o $@:$(LDFLAGS) -o $@:g' \ + -i src/makefile || die +} + +src_compile() { + emake \ + -e -C src \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + STRICT="" || die +} + +src_install() { + dobin src/last{al,db,ex} + exeinto /usr/share/${PN}/scripts + doexe scripts/* + dodoc doc/*.txt ChangeLog.txt README.txt +} diff --git a/sci-biology/last/last-299-r1.ebuild b/sci-biology/last/last-299-r1.ebuild new file mode 100644 index 000000000000..b6adee215970 --- /dev/null +++ b/sci-biology/last/last-299-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit toolchain-funcs python-single-r1 + +DESCRIPTION="Genome-scale comparison of biological sequences" +HOMEPAGE="http://last.cbrc.jp/" +SRC_URI="http://last.cbrc.jp/${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="app-arch/unzip" + +PATCHES=( + "${FILESDIR}"/${PN}-299-fix-build-system.patch + "${FILESDIR}"/${PN}-299-portable-shebangs.patch +) + +src_configure() { + tc-export CC CXX +} + +src_install() { + local DOCS=( doc/*.txt ChangeLog.txt README.txt ) + local HTML_DOCS=( doc/*html ) + einstalldocs + + dobin src/last{al,db,ex} + + cd scripts || die + local i + for i in *py; do + newbin ${i} ${i%.py} + done + dobin *sh +} diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/last/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest new file mode 100644 index 000000000000..fead05e00a48 --- /dev/null +++ b/sci-biology/mafft/Manifest @@ -0,0 +1,10 @@ +AUX 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$(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) + + makedirectionlist : $(OBJMAKEDIRECTIONLIST) +- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) + + setdirection : $(OBJSETDIRECTION) +- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) + + replaceu : $(OBJREPLACEU) +- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) + + restoreu : $(OBJRESTOREU) +- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(MYCFLAGS) -c gapfill.c +@@ -525,7 +525,7 @@ install : all + chmod 755 $(SCRIPTS) + $(INSTALL) $(SCRIPTS) $(BINDIR) + chmod 755 $(PROGS) +- $(INSTALL) -s $(PROGS) $(LIBDIR) ++ $(INSTALL) $(PROGS) $(LIBDIR) + $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) + + ( cd $(BINDIR); \ diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild new file mode 100644 index 000000000000..685d78005c73 --- /dev/null +++ b/sci-biology/mafft/mafft-7.050.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" +} + +src_compile() { + pushd core > /dev/null || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" + popd > /dev/null || die +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + pushd core + emake PREFIX="${ED}usr" install + popd + dodoc readme +} diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild new file mode 100644 index 000000000000..21761f1378e4 --- /dev/null +++ b/sci-biology/mafft/mafft-7.215.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { +# epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread +# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" + sed \ + -e 's:$(LDFLAGS)::g' \ + -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ + -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ + -e '/INSTALL/s: -s : :g' \ + -i core/Makefile || die +} + +src_compile() { + cd core || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + dodoc readme + cd core || die + emake PREFIX="${ED}usr" install +} diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild new file mode 100644 index 000000000000..92925d8342b2 --- /dev/null +++ b/sci-biology/mafft/mafft-7.305.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}/${P}${EXTENSIONS}" + +src_prepare() { + default + + append-cflags -Wno-unused-result + use threads && append-cppflags -Denablemultithread + + sed \ + -e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \ + -e 's:$(LDFLAGS)::g' \ + -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ + -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ + -e '/INSTALL/s: -s : :g' \ + -i core/Makefile || die +} + +src_compile() { + cd core || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die "Tests failed" + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die "Tests failed" + bash ../core/mafft --globalpair sample > test.gins1 || die "Tests failed" + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die "Tests failed" + bash ../core/mafft --localpair sample > test.lins1 || die "Tests failed" + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die "Tests failed" + + diff test.fftns2 sample.fftns2 || die "Tests failed" + diff test.fftnsi sample.fftnsi || die "Tests failed" + diff test.gins1 sample.gins1 || die "Tests failed" + diff test.ginsi sample.ginsi || die "Tests failed" + diff test.lins1 sample.lins1 || die "Tests failed" +} + +src_install() { + DOCS=( readme ) + einstalldocs + + cd core || die + emake PREFIX="${ED%/}/usr" install +} diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/mafft/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest new file mode 100644 index 000000000000..f26a3ced4353 --- /dev/null +++ b/sci-biology/maq/Manifest @@ -0,0 +1,10 @@ +AUX maq-0.7.1-bfr-overfl.patch 527 SHA256 ff7521f696d4deb311f3dec07997bd8cce068749369d6cd3d3e65fb6cce19e56 SHA512 953587e9354f2d3a070aae67ee999105b96678b2b781b9fbe8416d040a594d1db2ed6e7de0516cd29c2020de5129bbc26b78b7bfa5a258ebb5cb9fd4715f8bcf WHIRLPOOL ab41e0d61d75caf9780920eb87bd2def0b6b1006860b60d43d5fa8f96dc6a1956147073b2e6b186a64cb977c055a4e6133f12eb7d925aecf7c650a1cfdd3fed7 +AUX maq-0.7.1-flags.patch 799 SHA256 f1949b063ed015182e403668dc19466d079eacc6d351d11cc5d099d2aeeb18f9 SHA512 f13d8af7884691f2d8c8e9bd9d370c5ca12e863aaf05e156a964ba88053d86dcb63f24169fbc3b2a9264423510061c26d88904b87ea8aeb8bf446b51e190aedb WHIRLPOOL 6091105a0f1606bc96a5da85026da7dc4acf4d9900e9d26f64e353486eb3e1fc90862c5b16f3709a19019ace12313bb60af4e7603a4c8c49716f878c96486cfe +AUX maq-0.7.1-gcc-4.7.patch 1429 SHA256 df958693a9eb428069ca09410f549b22444fbd1818fab6101aaa03e658f00250 SHA512 e2936757fff7f32d8dea3da3181839b7b4190a15f4bfb5c3b6cb6a723a10ba8f6e4f762eca32387345a4263c9bf525a425d5e58c78f387a1813508fdc5fb364c WHIRLPOOL 244d7656f0ca1db364068910bd1042363ebcc7933506ad2e17c653e74e76ddc8b9862a2b84d82eed87aaa35776b964eaeaf70069f9e47418a1f3f850f3a91f4d +AUX maq-0.7.1-remove-64bit-flag.patch 787 SHA256 83b88bfc8f9035528460c5f194195bf33ccd9affb574e0a78198828143bee894 SHA512 4864453afa79679c253b17a2b125bf0b44c1a05a6ae6341821382991217026b599437288a1c96625cdc2a1fad2cf73c79798a230bbfccef46e1c92012a6c3df1 WHIRLPOOL f77db9e0358681e9e140004b74544754d8c91fbf254d11610610af4acbe5f1ba045127d93e00fffc8e7df2f36a5cea4e3b5641ed026d5f8a7aa67f7d9c6d79fe +DIST calib-36.dat.gz 196371 SHA256 d4480e04446eb273f1908add709dd5a24262c08a59a1647b9a2d053f4d30181b SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7 WHIRLPOOL cf060f27ba191f234f5db2a8c43a70bb03e4f9625fb73dcdcccdc342a9baa8686602fc92eaab5a68d4864d334852a90d665cc50421dacdf6257fb96f47f5829b +DIST maq-0.7.1.tar.bz2 368645 SHA256 e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2 SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c WHIRLPOOL 5e00112a0cca7646433b53f799e9baa088048f9b6b5577e3a633d23ac78c2d79169fe00f3d28ea7e304b73605b7e6a5c97e0d051881072955a936f1b3b0b8a21 +EBUILD maq-0.7.1-r2.ebuild 799 SHA256 1478f732dea1917bb9816dcec3cb2d967659a47e4f7069a9cc5a90c9fbdf4637 SHA512 5e52158937efbb822f9e521ec19b76a3dab1d6823da94cc154947d1024d2aa59bab00b111eb9d3d3e23a59782f2069ff4aa079133fa4608a4aa37e623e14c265 WHIRLPOOL 0c77259845a10adb180d6a6879934f30e09e87ba422539981c737e05d281c9dd3ab4539ff0663299053e41ec9a8b24487788af481ecfb4b35332245323c35911 +MISC ChangeLog 2569 SHA256 8678a35c30639699aa4992f76cc26d96a039e15b1ed73220307f251c40636fc1 SHA512 17db6913d41be3493da79df5015173007215efa4b8dd309bf7b8b826eea134460bbecd85a64c0c83a7ff2584e7aa5ec24aaa75ee5fb1dda40a295a160872cb37 WHIRLPOOL bd5b06241e6bb89c3db4f2fc711c96a9e9cad0436853005048499442569b95d0d340e42389b1c53df5ba83808f733a2669a83315835b90d5f91278d8d2383a4f +MISC ChangeLog-2015 1593 SHA256 11a721662c24da57a4547df5500eb4f67e45ba788b9c12ede57861992cadd88b SHA512 dcc4634336b513ef01f06c269d65c2b1ca55b6cc0436521cf552d6bdd7cafcb29617cba552ac0cbcbfcffea20154aa1c92b68ced341f3d9a423d9c9d7db2d99a WHIRLPOOL 55d882686d50124d8251fa3101361aa180feaf7db0dd254208e6661c7d83a3cee433bf12cb64c45ea2f0d6ae659e877a70b36088dc5b099a0c6f5aead25609cc +MISC metadata.xml 344 SHA256 e7635c034b39ae80b82be3d5b388b8cbe8642e948d699f8b7a208b75618f4991 SHA512 01962a043f6efd23e14570c486b43f89319c47d040fe94324b67e077cbc755435d236eb736e70c5fc582798c8765daa0f85a1f39a3d18ab27bff171fa7765e45 WHIRLPOOL 9d8641cdc4d97433980cd5f9366ddb94e44d1b179e75c5fc17b54a64d0e64e6b17076039efc9cb5c5449fa1439aa8185579afa5a7554472b400461d7f995f3d0 diff --git a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch new file mode 100644 index 000000000000..9f4247d441f5 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch @@ -0,0 +1,16 @@ + simulate.c | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/simulate.c b/simulate.c +index 788c440..67ba2ba 100644 +--- a/simulate.c ++++ b/simulate.c +@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres) + memset(wc_single, 0, 40); memset(tot_single, 0, 40); + memset(wc_pair, 0, 40); memset(tot_pair, 0, 40); + memset(abpair, 0, 4 * 256 * 10); +- memset(tc[2], 0, 4 * sizeof(int)); ++ memset(tc, 0, 4 * sizeof(int)); + while (maqmap_read1(fp, m1)) { + int is_correct; + bit32_t p1, p2; diff --git a/sci-biology/maq/files/maq-0.7.1-flags.patch b/sci-biology/maq/files/maq-0.7.1-flags.patch new file mode 100644 index 000000000000..721e53248b7a --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-flags.patch @@ -0,0 +1,24 @@ + configure.ac | 3 ++- + 1 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/configure.ac b/configure.ac +index ad2f1e6..4f9d7be 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -8,6 +8,7 @@ AC_PROG_CXX + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} ++user_CXXFLAGS=${CXXFLAGS} + generic_CFLAGS="-Wall" + ext_CFLAGS="" + case "${host_cpu}-${host_os}" in +@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread, [ --enable-shortreads use shortread mode], + AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], + [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}" +-CXXFLAGS=$CFLAGS ++CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}" + + AC_STDC_HEADERS + AC_CHECK_HEADER(zlib.h) diff --git a/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch new file mode 100644 index 000000000000..4b97da89be48 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch @@ -0,0 +1,34 @@ + stdhash.hh | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..16cd1a3 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -412,7 +412,7 @@ public: + inline bool insert(const keytype_t &key) { + __lh3_hash_base_class<keytype_t>::rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } + else ++(this->n_size); // then ret == 2 +@@ -493,7 +493,7 @@ public: + inline bool insert(const keytype_t &key, const valtype_t &val) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + vals[i] = val; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } +@@ -503,7 +503,7 @@ public: + inline bool insert(const keytype_t &key, valtype_t **q) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + *q = vals + i; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } diff --git a/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch new file mode 100644 index 000000000000..3bcbc2b5fd51 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch @@ -0,0 +1,19 @@ +Do not hardcode -m64 into the build system + +--- a/configure.ac ++++ b/configure.ac +@@ -21,12 +21,12 @@ + [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"], + [ext_CFLAGS="-arch i386 -arch ppc"]);; + 0) CFLAGS="-m64" +- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"], []);; ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""], []);; + esac;; + *) + AC_MSG_CHECKING([if gcc accepts -m64]) + CFLAGS="-m64" +- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])], ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""; AC_MSG_RESULT([yes])], + [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);; + esac + AC_ARG_ENABLE(experimental, [ --enable-experimental enable experimental features], diff --git a/sci-biology/maq/maq-0.7.1-r2.ebuild b/sci-biology/maq/maq-0.7.1-r2.ebuild new file mode 100644 index 000000000000..14b0284b7f58 --- /dev/null +++ b/sci-biology/maq/maq-0.7.1-r2.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.bz2 + mirror://sourceforge/${PN}/calib-36.dat.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="sys-libs/zlib" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-bfr-overfl.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-remove-64bit-flag.patch +) + +src_prepare() { + default + eautoreconf +} + +src_install() { + default + + insinto /usr/share/${PN} + doins "${WORKDIR}"/*.dat + + doman maq.1 + dodoc ${PN}.pdf +} diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml new file mode 100644 index 000000000000..0b39d2a8530d --- /dev/null +++ b/sci-biology/maq/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">maq</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest new file mode 100644 index 000000000000..105b15262568 --- /dev/null +++ b/sci-biology/maqview/Manifest @@ -0,0 +1,8 @@ +AUX 0.2.5-ldflags.patch 1335 SHA256 0876b98428f7964be91fb27f853458ba557ca8bf7eb313e416ece5a869a31efe SHA512 ae034ae1279e49c71f9daf658aece35063c56afc7ac3269d21d21a2f5b6f8e7974be48c82b52f4d250a9dcacfd5e8c9208b40c904ff73af8592c7f39395c6b6e WHIRLPOOL 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40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6 WHIRLPOOL 0ba5a15a1317b4bb78458b9e282348983be9e2c30980aef4e35a9f5dacfff57226eaa4403fb0b9d9d448ba033409d548db224ed544ad365226a8fb59be8b743e +EBUILD maqview-0.2.5-r3.ebuild 608 SHA256 719fe87c607582da8c2b6cf50f9dd0296b5b935b2fd70bb28dac877b1e5d8d20 SHA512 71d33765c88d05e9d2c9c24c7d3bed6cefc194bbb4844a274ccb5b16380d8e1608acfb929b9dd8631adf9542ee3af5bcfd1cfed50f420b2d352d9b0d31eaf7bf WHIRLPOOL f590b13a08d314b3bfab5790f98707966cc10f8e6b582035ae7b7fa4c22ac5839bcc90d6b87f841260be19b8864c4b57d3882e9f5466f3ceea8fd325ba70d162 +MISC ChangeLog 2526 SHA256 c6ff0d1b78a0da57fd34e3779221f644aadfc9b5ff5e469b14616d2120701763 SHA512 b3a8b31668d4af69db4daea90f302c39b42b57e22a2c48eb64cf44405070ced1af360a70f48b49efd265c47b0480aa0d53693dbccf0871e6da62e1977e3b859a WHIRLPOOL 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index 000000000000..92b9a3ed58ac --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-ldflags.patch @@ -0,0 +1,46 @@ + configure.ac | 18 +++--------------- + 1 files changed, 3 insertions(+), 15 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 90e612b..5a00d15 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -9,17 +9,10 @@ AC_PROG_INSTALL + AC_STDC_HEADERS + + is_static=0 +-case ${prefix} in +- NONE);; +- *) is_static=1 +- AC_MSG_WARN([Library libglut will be statically linked.]) +- LDFLAGS="-L${prefix}/lib" +- CPPFLAGS="-I${prefix}/include";; +-esac + + # set CFLAGS and LDFLAGS + +-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS" ++true_CFLAGS="-DMAQ_LONGREADS" + case "${host_os}" in + darwin*) + GLLIBS="-framework OpenGL -framework GLUT" +@@ -30,17 +23,12 @@ case "${host_os}" in + i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";; + esac + AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"]) +- AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)], +- [is_static=1]) +- case $is_static in +- 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";; +- 0) GLLIBS="-lGL -lglut -lm";; +- esac ++ GLLIBS="-lGL -lglut -lm -lGLU" + AC_SUBST([GLLIBS]);; + # *) AC_MSG_ERROR([OS is not supported]);; + esac + AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1]) +-CFLAGS=$true_CFLAGS ++CFLAGS="${CFLAGS} $true_CFLAGS" + + AC_CONFIG_FILES([Makefile]) + AC_OUTPUT diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch new file mode 100644 index 000000000000..cd35273de66b --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-zlib.patch @@ -0,0 +1,33 @@ + Makefile.am | 6 +++--- + zrio.c | 2 +- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index dad515a..9617eb7 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,8 +1,8 @@ + bin_PROGRAMS = zrio maqindex maqview maqindex_socks +-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \ +- infback.c inftrees.c trees.c uncompr.c zutil.c +-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src) ++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c ++LIBS = -lz + zrio_SOURCES = zrio_main.c $(generic_src) ++zrio_LDADD = -lz + maqindex_SOURCES = maqmap_index_main.c $(generic_src) + maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \ + $(generic_src) +diff --git a/zrio.c b/zrio.c +index ffed00a..fe744df 100644 +--- a/zrio.c ++++ b/zrio.c +@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void + totin += strm.avail_in; + totout += strm.avail_out; + tmp = strm.avail_out; +- ret = inflate_zr(&strm, Z_BLOCK); /* return at end of block */ ++ ret = inflate(&strm, Z_BLOCK); /* return at end of block */ + totin -= strm.avail_in; + totout -= strm.avail_out; + if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout); diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch new file mode 100644 index 000000000000..043208bb79b5 --- /dev/null +++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch @@ -0,0 +1,16 @@ + stdhash.hh | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..f22c5a6 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -493,7 +493,7 @@ public: + inline bool insert(const keytype_t &key, const valtype_t &val) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + vals[i] = val; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } diff --git a/sci-biology/maqview/maqview-0.2.5-r3.ebuild b/sci-biology/maqview/maqview-0.2.5-r3.ebuild new file mode 100644 index 000000000000..2d6574217029 --- /dev/null +++ b/sci-biology/maqview/maqview-0.2.5-r3.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI="mirror://sourceforge/maq/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + media-libs/freeglut + sys-libs/zlib" +RDEPEND="${DEPEND} + sci-biology/maq" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-zlib.patch + "${FILESDIR}"/${P}-gcc4.7.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml new file mode 100644 index 000000000000..0b39d2a8530d --- /dev/null +++ b/sci-biology/maqview/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">maq</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest new file mode 100644 index 000000000000..adca26eb831f --- /dev/null +++ b/sci-biology/mcl/Manifest @@ -0,0 +1,10 @@ +AUX mcl-14.137-qa-implicit-declarations.patch 786 SHA256 ee30112d296b8ebbfd1b7f9b831aaed715aead47cab1c8756e9a68e05462b6e2 SHA512 e1388441e06075e951a1ff9994a8e9fe1083042c09e072c68e9abb20dc4a83498eb4cb71aa71d738268a50a0e03ee8e7976df9bbb304b8c90314d682bb8625d3 WHIRLPOOL fd024ef468fd8557f6e931b147c4a280c679482d8d55b80325146a1b1347f2212a6c4d02a90a90c46bd892e7a4e716cae332827486ebf58ff4c4aa2be8ab492d +DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e +DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279 +DIST mcl-14-137.tar.gz 3035491 SHA256 b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2 WHIRLPOOL 6a4afda86cc91c3ddacb64740f020cec2235e22411430281cde9106fb8399663c7854eb1ba5f477624d825280a7762cf5a3f7c6ec824a784a7e200e92d42a168 +EBUILD mcl-08.312.ebuild 678 SHA256 4dba82220a12bd139e76a72622b3896c30db75ebf907a7ceb0f5b4a88a9bac6c SHA512 e628f2226efd505d191efdaac7a9f83e896d5b97455833aa7a6846fc7a8c8a1079fcc60fc343606252e839a3a2820dc6ab53ad84d57ae582f339b840bfbe9cc6 WHIRLPOOL 6780bc68f9f644f98faa82162b69032366f33c9f0ac3ecd8026aa411a2decda8e7620663e4535ca3328250eed4609cbf2cbfaa258db959a9d49799aa6f57dedc +EBUILD mcl-12.135.ebuild 678 SHA256 4dba82220a12bd139e76a72622b3896c30db75ebf907a7ceb0f5b4a88a9bac6c SHA512 e628f2226efd505d191efdaac7a9f83e896d5b97455833aa7a6846fc7a8c8a1079fcc60fc343606252e839a3a2820dc6ab53ad84d57ae582f339b840bfbe9cc6 WHIRLPOOL 6780bc68f9f644f98faa82162b69032366f33c9f0ac3ecd8026aa411a2decda8e7620663e4535ca3328250eed4609cbf2cbfaa258db959a9d49799aa6f57dedc +EBUILD mcl-14.137.ebuild 651 SHA256 6fe7f4adc04598fb1df491d4048a8a51d620799cdd047ad6f226b01d09fbf92f SHA512 042277297965d4796d0805dad2a951e8bd467630c7904fe1a5211616fc2a620c041ea6093bbaf10e6fed17037bccd7013afcfb0260e69c09bd1cdc3ca2f76f53 WHIRLPOOL effe1116b79cf9c2b8194bb69e048242860443a01d27889c151f6750e780ba116455fd598240feba62a7385897be7b7b879834dc0edd4c801320f8b8b5066f4c +MISC ChangeLog 2694 SHA256 b9b528bf475eb8d8d0f8cfce2efcd07e83b408ec8a3cf1b783755860412ff6c8 SHA512 a0256b62909e040eb9a9b01b379e49812ec776c353f5bb82ccda08a4aba5c6a7c98efd0e5144363c580f257ae58c3eb20fc4033d93b25fb5ccbd9cbd1496c184 WHIRLPOOL ec83d61d3a139b8ae37c02121fcfa08acd42503f299aa0a0ad4150989f98053ddf01f26cd23cfc31e646d1ddc3c7a449ea243233f984209d721ccdd381c77c9e +MISC ChangeLog-2015 910 SHA256 af9af086bd09e35b484f10cb43a649c4a398ae12ba7ee99de86786c312f182d9 SHA512 e615f431461784a2fef5c9ef7f445ef40bda238ed47f07a277acae33ec2e629b68d98cde0a9ea99cb3f32923ec71508fcc4047c36dea9e70f2fd81ac99301354 WHIRLPOOL 4f6659d92ee95f174e567038cf33bf7e5c99b36fb29b98f50275c3924b2f33d30ad76c5fd711a96eb3262bc2de0974c8690fbb487c50d6633039a7309599e4f5 +MISC metadata.xml 351 SHA256 fecfcf8c3f170513b7e1d3dd8f505846f2728a2f9d4eb14bdb4260788ca05f5f SHA512 cbd1dc5b22ba9761f793edffa5adc3a5c99fe99569301bbba219f04ba21c603e8a3c183d04ab6838ebab3777b2855a2d46a69908e683f5183a5a22872dd429dd WHIRLPOOL 1773bdfcb553cb970fc1cf94fde6526c72187e15a30aca6823954e355cac413c414b7f2746e16875635c30299b6f918e779de8b0b5084439ceab633323f56b61 diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch new file mode 100644 index 000000000000..df4309874d48 --- /dev/null +++ b/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch @@ -0,0 +1,27 @@ +Fix QA issues related to implicit declarations. + +* QA Notice: Package triggers severe warnings which indicate that it +* may exhibit random runtime failures. +* clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration] +* mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration] + +--- mcl-14-137/src/shcl/clmadjust.c ++++ mcl-14-137/src/shcl/clmadjust.c +@@ -14,6 +14,7 @@ + #include "report.h" + #include "clmadjust.h" + ++#include "util/alloc.h" + #include "util/io.h" + #include "util/types.h" + #include "util/err.h" +--- mcl-14-137/src/shmcx/mcxi.c ++++ mcl-14-137/src/shmcx/mcxi.c +@@ -8,6 +8,7 @@ + */ + + #include <stdio.h> ++#include <unistd.h> + + #include "stack.h" + #include "glob.h" diff --git a/sci-biology/mcl/mcl-08.312.ebuild b/sci-biology/mcl/mcl-08.312.ebuild new file mode 100644 index 000000000000..fb0bf237a671 --- /dev/null +++ b/sci-biology/mcl/mcl-08.312.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +MY_P="${PN}-${PV/./-}" + +DESCRIPTION="A Markov Cluster Algorithm implementation" +HOMEPAGE="http://micans.org/mcl/" +SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+blast" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find \ + -name Makefile.am \ + -exec sed \ + -e '/docdir/d' \ + -e '/exampledir/s:doc::g' \ + -i '{}' + || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( $(use_enable blast) ) + autotools-utils_src_configure +} diff --git a/sci-biology/mcl/mcl-12.135.ebuild b/sci-biology/mcl/mcl-12.135.ebuild new file mode 100644 index 000000000000..fb0bf237a671 --- /dev/null +++ b/sci-biology/mcl/mcl-12.135.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +MY_P="${PN}-${PV/./-}" + +DESCRIPTION="A Markov Cluster Algorithm implementation" +HOMEPAGE="http://micans.org/mcl/" +SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+blast" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find \ + -name Makefile.am \ + -exec sed \ + -e '/docdir/d' \ + -e '/exampledir/s:doc::g' \ + -i '{}' + || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( $(use_enable blast) ) + autotools-utils_src_configure +} diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild new file mode 100644 index 000000000000..e48198deca29 --- /dev/null +++ b/sci-biology/mcl/mcl-14.137.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +MY_P="${PN}-${PV/./-}" + +DESCRIPTION="A Markov Cluster Algorithm implementation" +HOMEPAGE="http://micans.org/mcl/" +SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+blast" + +PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch") +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find \ + -name Makefile.am \ + -exec sed \ + -e '/docdir/d' \ + -e '/exampledir/s:doc::g' \ + -i '{}' + || die + default + eautoreconf +} + +src_configure() { + econf $(use_enable blast) +} diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml new file mode 100644 index 000000000000..a8e52b205b3a --- /dev/null +++ b/sci-biology/mcl/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="blast"> + add support for NCBI BLAST data + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest new file mode 100644 index 000000000000..81c0e1d7302c --- /dev/null +++ b/sci-biology/meme/Manifest @@ -0,0 +1,8 @@ +AUX meme-4.11.2_p2-fix-build-system.patch 10447 SHA256 e8fabb881c4b2f24c7ebff9c245aafeb55a4d80db349df067d09d0143195f36e SHA512 85181e114e825081ef52545fef7ab638c91029964eb8be2e1e4042d1d766d5376dbcabc9bd3902f19d162997dd63cb02fea66d231df6bafc0e74981373ea9724 WHIRLPOOL ffa36e94450f9c6752b8e9b6c4b03f9a1ac2d4cabbf4a90bb138c4a0ab2dda4549023b3175c1a2375ac3cba3121681c88cd5ad9773111b49feda2972898a7677 +AUX meme-4.11.2_p2-patch1.patch 13820 SHA256 2cad7e80d00c5b493bcb60a56921e909e4168015d57daf87ac708d1404b59756 SHA512 5a5989b5c626dee6aeaa435ce6c444caed6711d62216743d97215abddef95eb92c66544576866fc43c8efb090410aaed425231642dfcd9634b3f3025d5f1981f WHIRLPOOL 739f4ce6b7b8d9a3649ec262aed66077f60f43629c4be0b8d3ce99d55656272e6dfa21490aee2159e203de113d16f6b48fa9458055215e326dfc0eedaf876f02 +AUX meme-4.11.2_p2-patch2.patch 1684 SHA256 b6bd7747e7995da169d40b9d0101c3a1d7658edbc98917f1f5b120202aab50ad SHA512 9c9b01196f76e3b02fa40c7a4d20bc77622cc3ac188584a53774be4ad72a889a72a7a57b38dda81fc7f1bb23db20eec50b0778b71caade4ddf65e49407f3ef8a WHIRLPOOL df198af71851937b3c3f1cd780e30a850f5a462ac94271898b176abcba64c20cedfc61080770f02b4f45b56ed00a604b0011576dc0e0f40330a28ca362b60f27 +DIST meme_4.11.2.tar.gz 18004930 SHA256 6e3ff843366588ea13fa8060306be9e2c144521912dfb268f03638003bcdd581 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 WHIRLPOOL 6b77d7832342658d5cf546af0b005b59664c811d25a0412df765a15a8c80a75d9618a1f9966c9a2824750eced6605b534d41199382a6f2641e7430540ba19fcf +EBUILD meme-4.11.2_p2.ebuild 2352 SHA256 e020a0a81f04af2804748a61e76c1c583daf6aef5e57928277c649458877a734 SHA512 fa4bd73f96f5f0f05dbbd12d316abe49d0414978cbcdc25bb625c288feb346d979c955316298489d951430faf60354f380ead663d04e5e711789e67d6be52e63 WHIRLPOOL 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91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch new file mode 100644 index 000000000000..b548de5a39a5 --- /dev/null +++ b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch @@ -0,0 +1,346 @@ +Fix and modernise build system +* Remove all *FLAGS setting, just append to the user-supplied ones +* Add --enable-doc and --enable-examples configure flags +* Install documentation and examples in correct directories +* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES +* Install python and perl modules correctly + +--- a/configure.ac ++++ b/configure.ac +@@ -76,61 +76,10 @@ + AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no]) + + # Check for compiler-specific settings +-LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` +-if test "${GCC}" = "yes"; then +- ac_cc_opt="-O3" +- ac_cc_debug_opt="-O0" +- ac_cc_warn="-Wall -Wno-unused" +- ac_cc_debug="-ggdb" +- # Check for OS X llvm (clang) compiler +- if `gcc --version |grep llvm >/dev/null`; then +- ac_cc_debug="-g" +- fi +- CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" +-else +- ac_cc_opt="-O" +- ac_cc_debug_opt="" +- ac_cc_warn="" +- ac_cc_debug="-g" +- CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" +-fi +- +-# Set up default libxml2 settings +-# check for installed copy of libxml2 +-build_libxml2="yes" +-if test -n "$XML2_CONFIG"; then +- # Require at least version 2.6 +- required_libxml2_version="2006000" +- LIBXML2_VERSION="`$XML2_CONFIG --version | \ +- awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`" +- if test -n "$LIBXML2_VERSION" && \ +- test "$LIBXML2_VERSION" -ge "$required_libxml2_version"; then +- build_libxml2="no" +- LIBXML2_LIBS="`$XML2_CONFIG --libs`" +- LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`" +- fi +-fi +-if test -z "$LIBXML2_LIBS"; then +- AC_MSG_WARN([libxml2 library not found]) +- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" +- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" +-fi +- +-# Set up default libxslt settings +-# check for installed copy of libxslt +-build_libxslt="yes" +-if test -n "$XSLT_CONFIG"; then +- build_libxslt="no" +- LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt" +- LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`" +-fi +-if test -z "$LIBXSLT_LIBS"; then +- AC_MSG_WARN([libxslt library not found]) +- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" +- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" +- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" +- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" +-fi ++AC_PROG_MKDIR_P ++AC_SYS_LARGEFILE ++CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}" ++CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}" + + # who is installing + USER=`whoami` +@@ -279,6 +227,16 @@ + AM_CONDITIONAL(PARALLEL, test ["$parallel" != no]) + AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) + ++dnl Documentation ++AC_ARG_ENABLE([doc], ++ AS_HELP_STRING([--enable-doc], [Enable installation of documentation])) ++AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"]) ++ ++dnl Examples ++AC_ARG_ENABLE([examples], ++ AS_HELP_STRING([--enable-examples], [Enable installation of examples])) ++AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"]) ++ + AC_ARG_ENABLE( + webservice, + [ --enable-webservice=deploy_dir Deploy the MEME service on an existing Opal 2.5+ installation], +@@ -309,24 +267,35 @@ + AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"]) + + # enable building of included libxml2 +-AC_ARG_ENABLE( +- build_libxml2, +- [ --enable-build-libxml2 Build included version of libxml2. Default is to use pre-existing locally installed copy.], +- build_libxml2=$enableval; \ +- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \ +- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , ) +-AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes]) ++AC_ARG_ENABLE([build-libxml2], ++ AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.])) ++AS_IF([test "x$enable_build_libxml2" = "xyes"], [ ++ dnl Enable building of bundled libs ++ LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" ++ LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" ++ ],[ ++ dnl Use system libraries ++ PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6]) ++]) ++AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"]) ++ + + # enable building of included libxslt +-AC_ARG_ENABLE( +- build_libxslt, +- [ --enable-build-libxslt Build included version of libxslt. Default is to use pre-existing locally installed copy.], +- build_libxslt=$enableval; \ +- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \ +- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \ +- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \ +- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , ) +-AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes]) ++AC_ARG_ENABLE([build-libxslt], ++ AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.])) ++AS_IF([test "x$enable_build_libxslt" = "xyes"], [ ++ dnl Enable building of bundled libs ++ LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" ++ LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" ++ ++ LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" ++ LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" ++ ],[ ++ dnl Use system libraries ++ PKG_CHECK_MODULES([LIBXSLT], [libxslt]) ++ PKG_CHECK_MODULES([LIBEXSLT], [libexslt]) ++]) ++AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"]) + + # set website url + AC_ARG_WITH( +@@ -427,13 +396,13 @@ + [AC_PATH_PROG(PERL, perl)]) + AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] ) + ++AC_ARG_WITH([perl-dir], ++ AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"]) ++AC_SUBST([perlmoddir]) ++ ++ + # set path to Python +-AC_ARG_WITH( +- python, +- [ --with-python=NAME Set path to Python. Default is to take from user's PATH.], +- [PYTHON=$withval], +- [AC_PATH_PROG(PYTHON, python)]) +-AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] ) ++AM_PATH_PYTHON + + # set path to convert utility + AC_ARG_WITH( +@@ -586,13 +555,15 @@ + Configuration parameters + ======================== + +- Install path: ${prefix} ++ Install path (prefix): ${prefix} + Install UID: ${MEME_USER} + Version: ${VERSION} +- C compiler: ${CC} +- C compiler flags: ${CFLAGS} +- Linker: ${LD} +- Special Libs: ${LIBS} ++ C compiler (CC): ${CC} ++ C compiler flags (CFLAGS): ${CFLAGS} ++ C preproc flags (CPPFLAGS): ${CPPFLAGS} ++ Linker (LD): ${LD} ++ Linker flags (LDFLAGS): ${LDFLAGS} ++ Special Libs (LIBS): ${LIBS} + MPICC ${MPICC} + MPIRUN ${MPIRUN} + MPI_CMD ${MPI_CMD} +--- a/doc/css/Makefile.am ++++ b/doc/css/Makefile.am +@@ -5,7 +5,7 @@ + + EXTRA_DIST = $(NORMAL_FILES) + +-if ! WEBSITE +-doccssdir = $(prefix)/doc/css ++if ENABLE_DOC ++doccssdir = $(htmldir)/css + doccss_DATA = $(NORMAL_FILES) + endif +--- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am ++++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am +@@ -7,8 +7,8 @@ + EXAMPLES = \ + prior.dist.txt + +-if ! WEBSITE +-exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files ++if ENABLE_EXAMPLES ++exdir = $(docdir)/examples/compute_prior_dist_example_output_files + ex_DATA = $(EXAMPLES) + endif + +--- a/doc/examples/Makefile.am ++++ b/doc/examples/Makefile.am +@@ -22,8 +22,8 @@ + # load the EXAMPLE_OUTPUT_FILES variable + include examples.mk + +-if ! WEBSITE +-exdir = $(prefix)/doc/examples ++if ENABLE_EXAMPLES ++exdir = $(docdir)/examples + nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES) + endif + +--- a/doc/examples/sample_opal_scripts/Makefile.am ++++ b/doc/examples/sample_opal_scripts/Makefile.am +@@ -15,8 +15,8 @@ + MemeClient.pl \ + MemeClient.py + +-if ! WEBSITE +-exdir = $(prefix)/doc/examples/sample_opal_scripts ++if ENABLE_EXAMPLES ++exdir = $(docdir)/examples/sample_opal_scripts + ex_DATA = $(EXAMPLES) + endif + +--- a/doc/images/Makefile.am ++++ b/doc/images/Makefile.am +@@ -30,8 +30,8 @@ + + MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES) + +-if ! WEBSITE +-memeimgdir = $(prefix)/doc/images ++if ENABLE_DOC ++memeimgdir = $(htmldir)/images + memeimg_DATA = $(MEME_IMAGES) + endif + +--- a/doc/js/Makefile.am ++++ b/doc/js/Makefile.am +@@ -41,8 +41,8 @@ + + BUILT_SOURCES = $(BUILT_FILES) + +-if ! WEBSITE +-docjsdir = $(prefix)/doc/js ++if ENABLE_DOC ++docjsdir = $(htmldir)/js + docjs_DATA = $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES) + endif + +--- a/doc/Makefile.am ++++ b/doc/Makefile.am +@@ -129,8 +129,8 @@ + update-sequence-db.html \ + ismb94.pdf + +-if ! WEBSITE +-memedocdir = $(prefix)/doc ++if ENABLE_DOC ++memedocdir = $(htmldir) + memedoc_DATA = $(NORMAL_FILES) + endif + +--- a/Makefile.am ++++ b/Makefile.am +@@ -52,7 +52,7 @@ + endif + + dbdir: +- mkdir -p $(MEME_DB) ++ $(MKDIR_P) $(DESTDIR)/$(MEME_DB) + + all-local: + if WEBSITE +@@ -64,8 +64,8 @@ + endif + + install-data-local: +- mkdir -p $(MEME_LOGS) +- chmod a+w $(MEME_LOGS) ++ $(MKDIR_P) $(DESTDIR)/$(MEME_LOGS) ++ chmod a+w $(DESTDIR)/$(MEME_LOGS) + + distdir = $(PACKAGE)_$(VERSION) + +--- a/scripts/Makefile.am ++++ b/scripts/Makefile.am +@@ -22,8 +22,8 @@ + -e 's%@WHICHJAVA@%$(JAVA)%' \ + -e 's%@WHICHCONVERT@%$(CONVERT)%' \ + -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \ +- -e 's%@PERLLIBDIR@%$(libdir)/perl%' \ +- -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \ ++ -e 's%@PERLLIBDIR@%$(perlmoddir)%' \ ++ -e 's%@PYTHONLIBDIR@%$(pythondir)%' \ + -e 's%@JAVALIBDIR@%$(libdir)/java%' \ + -e 's%@LAM_BIN@%$(LAMBIN)%' \ + -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \ +@@ -62,7 +62,7 @@ + DiffXML.pm \ + HypergeometricDynProg.pm + +-perlmoddir=$(libdir)/perl ++perlmoddir = $(exec_prefix)/@perlmoddir@ + perlmod_SCRIPTS = \ + $(BUILT_PERL_MOD) \ + $(NORMAL_PERL_MOD) +@@ -76,8 +76,7 @@ + hypergeometric.py \ + sequence.py + +-pythonlibdir=$(libdir)/python +-pythonlib_SCRIPTS = \ ++python_PYTHON = \ + $(BUILT_PYTHON_LIB) \ + $(NORMAL_PYTHON_LIB) + +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -19,7 +19,13 @@ + ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION) + ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE) + +-SUBDIRS = filters libxml2 libxslt libexslt . parallel ++SUBDIRS = filters . parallel ++if BUILD_LIBXML2 ++SUBDIRS += libxml2 ++endif ++if BUILD_LIBXSLT ++SUBDIRS += libxslt libexslt ++endif + + BUILT_SOURCES = dir.h projrel.h + diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch new file mode 100644 index 000000000000..30a182f8f43a --- /dev/null +++ b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch @@ -0,0 +1,383 @@ +--- a/doc/alphabet-format.html ++++ b/doc/alphabet-format.html +@@ -233,7 +233,7 @@ + providing a reference on the meaning of the symbols used. If present, the + symbol name must be the second field.</p> + <p>The "<span class="pdat">name</span>" follows the rules of +- <a href="qstr">quoted text</a>.</p> ++ <a href="#qstr">quoted text</a>.</p> + </div> + <h5>color</h5> + <div class="indent"> +--- a/doc/release-notes.html ++++ b/doc/release-notes.html +@@ -14,8 +14,26 @@ + <h2>Motif-based sequence analysis tools</h2> + </div> + <h2>MEME Suite Release Notes</h2> ++ <hr> ++ <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b> ++ <ul> ++ <li> ++ <b>Bug fixes</b> ++ <ul> ++ <li> ++ Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate ++ reading the sequence file. ++ </li> ++ <li> ++ Modified MEME to fall back to a simple Dirichlet prior when ++ using DNA or a custom alphabet with a prior that requires ++ a prior library, but no prior libray is specified. ++ </li> ++ </ul ++ </li> ++ </ul> ++ <p> + <hr> +- <p> + <b>MEME version 4.11.2 -- May 5 2016</b> + </p> + <ul> +--- a/src/fasta-io.c ++++ b/src/fasta-io.c +@@ -14,6 +14,7 @@ + #include "alphabet.h" + #include "fasta-io.h" + #include "io.h" ++#include "seq-reader-from-fasta.h" + #include "prior-reader-from-psp.h" + #include "seq.h" + +@@ -159,61 +160,6 @@ + } + + /**************************************************************************** +- * Read raw sequence until a new sequence is encountered or too many letters +- * are read. The new sequence is appended to the end of the given +- * sequence. +- * +- * Return: Was the sequence read completely? +- ****************************************************************************/ +-static BOOLEAN_T read_raw_sequence_from_reader( +- DATA_BLOCK_READER_T *fasta_reader, // Sequence source +- char* name, // Sequence ID (used in error messages). +- ALPH_T* alph, // Alphabet in use +- unsigned int offset, // Current position in raw_sequence. +- unsigned int max_chars, // Maximum chars in raw_sequence. +- char* raw_sequence // Pre-allocated sequence. +-) { +- // tlb; change a_char to integer so it will compile on SGI +- int a_char; +- int start_update; +- BOOLEAN_T return_value = TRUE; +- +- // Start at the end of the given sequence. +- assert(offset < max_chars); +- +- DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset); +- return_value = !fasta_reader->get_next_block(fasta_reader, seq_block); +- +- char *seq_buffer = get_sequence_from_data_block(seq_block); +- size_t seq_buffer_size = get_num_read_into_data_block(seq_block); +- int i; +- for (i = 0; i < seq_buffer_size; ++i) { +- a_char = seq_buffer[i]; +- // Skip non-alphabetic characters. +- if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') { +- if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) { +- fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n", +- a_char, name); +- } +- } else { +- // skip check if unknown alph +- if (alph != NULL && !alph_is_known(alph, a_char)) { +- fprintf(stderr, "Warning: Converting illegal character %c to %c ", +- a_char, alph_wildcard(alph)); +- fprintf(stderr, "in sequence %s.\n", name); +- a_char = alph_wildcard(alph); +- } +- raw_sequence[offset] = (char) a_char; +- ++offset; +- } +- } +- +- raw_sequence[offset] = '\0'; +- free_data_block(seq_block); +- return(return_value); +-} +- +-/**************************************************************************** + * Read one sequence from a file in Fasta format. + * + * Return: Was a sequence successfully read? +@@ -320,44 +266,6 @@ + } + + /**************************************************************************** +- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder +- * and copy them in to the raw sequence in the SEQ_T object starting at the +- * given buffer offset. +- ****************************************************************************/ +-void read_one_fasta_segment_from_reader( +- DATA_BLOCK_READER_T *fasta_reader, +- size_t max_size, +- size_t buffer_offset, +- SEQ_T *sequence +-) { +- +- assert(sequence != NULL); +- assert(get_seq_length(sequence) <= max_size); +- +- // Get the raw sequence buffer from the SEQ_T +- char *raw_sequence = get_raw_sequence(sequence); +- if (raw_sequence == NULL) { +- // Allocate space for raw sequence if not done yet. +- raw_sequence = mm_malloc(sizeof(char) * max_size + 1); +- raw_sequence[0] = 0; +- } +- +- // Read a block of sequence charaters into the +- // raw sequence buffer for the SEQ_T. +- char *name = get_seq_name(sequence); +- BOOLEAN_T is_complete = read_raw_sequence_from_reader( +- fasta_reader, +- name, +- NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable! +- buffer_offset, +- max_size, +- raw_sequence +- ); +- set_raw_sequence(raw_sequence, is_complete, sequence); +- +-} +- +-/**************************************************************************** + * Read all the sequences from a FASTA file at once. + Multiple files can be appended by calling this more than once. + ****************************************************************************/ +--- a/src/fasta-io.h ++++ b/src/fasta-io.h +@@ -43,19 +43,6 @@ + ); + + /**************************************************************************** +- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder +- * and copy them in to the raw sequence in the SEQ_T object starting at the +- * given buffer offset. +- ****************************************************************************/ +-void read_one_fasta_segment_from_reader( +- DATA_BLOCK_READER_T *fasta_reader, +- size_t max_size, +- size_t buffer_offset, +- SEQ_T* sequence +-); +- +- +-/**************************************************************************** + * Read all the sequences from a file in Fasta format. + ****************************************************************************/ + void read_many_fastas +--- a/src/init.c ++++ b/src/init.c +@@ -767,10 +767,16 @@ + if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins + plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB); + } else { +- fprintf(stderr, "The prior library must be specified for DNA or custom " +- "alphabets when specifiying a prior type of 'dmix', 'mega' " +- "or 'megap'."); +- exit(1); ++ fprintf( ++ stderr, ++ "WARNING: When using DNA or a custom alphabet, " ++ "and specifiying a prior type of\n" ++ "'dmix', 'mega' or 'megap', a prior library must be provided.\n" ++ "No prior library was provided, so a simple Dirichlet prior will be used.\n" ++ ); ++ prior = "dirichlet"; ++ ptype = Dirichlet; ++ if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet + } + } + } +--- a/src/seq-reader-from-fasta.c ++++ b/src/seq-reader-from-fasta.c +@@ -639,11 +639,140 @@ + return fasta_reader->current_position; + } + ++ ++/**************************************************************************** ++ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder ++ * and copy them in to the raw sequence in the SEQ_T object starting at the ++ * given buffer offset. ++ ****************************************************************************/ ++void read_one_fasta_segment_from_reader( ++ DATA_BLOCK_READER_T *fasta_reader, ++ size_t max_size, ++ size_t offset, ++ SEQ_T *sequence ++) { ++ ++ ++ assert(sequence != NULL); ++ assert(offset < max_size); ++ ++ // Get the raw sequence buffer from the SEQ_T ++ char *raw_sequence = get_raw_sequence(sequence); ++ if (raw_sequence == NULL) { ++ // Allocate space for raw sequence if not done yet. ++ raw_sequence = mm_malloc(sizeof(char) * max_size + 1); ++ raw_sequence[0] = 0; ++ } ++ ++ // Read a block of sequence charaters into the ++ // raw sequence buffer for the SEQ_T, starting at offset. ++ BOOLEAN_T is_complete = read_raw_sequence_from_reader( ++ fasta_reader, ++ max_size - offset, ++ raw_sequence + offset ++ ); ++ set_raw_sequence(raw_sequence, is_complete, sequence); ++} ++ ++/**************************************************************************** ++ * Read raw sequence until a new sequence is encountered or too many letters ++ * are read. ++ * ++ * Return: Was the sequence read completely? ++ ****************************************************************************/ ++BOOLEAN_T read_raw_sequence_from_reader( ++ DATA_BLOCK_READER_T *reader, // Sequence source ++ unsigned int max_chars, // Maximum chars in raw_sequence. ++ char* raw_sequence // Pre-allocated sequence buffer. ++) { ++ ++ SEQ_READER_FROM_FASTA_T *fasta_reader ++ = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader); ++ ++ // Read sequence into temp. buffer from the sequence file. ++ char buffer[max_chars]; ++ long start_file_pos = ftell(fasta_reader->fasta_file); ++ size_t seq_index = 0; ++ size_t total_read = 0; ++ while (seq_index < max_chars) { ++ ++ size_t num_char_read = fread( ++ buffer, ++ sizeof(char), ++ max_chars - seq_index, ++ fasta_reader->fasta_file ++ ); ++ fasta_reader->current_position += num_char_read; ++ total_read += num_char_read; ++ ++ if (feof(fasta_reader->fasta_file)) { ++ fasta_reader->at_end_of_file = TRUE; ++ } ++ else if (num_char_read < (max_chars - seq_index)) { ++ die( ++ "Error while reading sequence from file:%s.\nError message: %s\n", ++ fasta_reader->filename, ++ strerror(ferror(fasta_reader->fasta_file)) ++ ); ++ } ++ ++ size_t i; ++ for(i = 0; i < num_char_read; ++i) { ++ char c = buffer[i]; ++ assert(c != 0); ++ if (isspace(c)) { ++ // Skip over white space ++ fasta_reader->at_start_of_line = (c == '\n'); ++ } ++ else if (c == '>' && fasta_reader->at_start_of_line == TRUE) { ++ // We found the start of a new sequence while trying ++ // to fill the buffer. Leave the buffer incomplete. ++ // and wind back the file ++ fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET); ++ fasta_reader->current_position = start_file_pos + i - 1; ++ fasta_reader->at_end_of_seq = TRUE; ++ fasta_reader->at_start_of_line = FALSE; ++ fasta_reader->at_end_of_file = FALSE; ++ break; ++ } ++ else { ++ fasta_reader->at_start_of_line = FALSE; ++ // Check that character is legal in alphabet. ++ // If not, replace with wild card character. ++ if (alph_is_known(fasta_reader->alphabet, c)) { ++ raw_sequence[seq_index] = c; ++ } ++ else { ++ raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet); ++ fprintf( ++ stderr, ++ "Warning: %c is not a valid character in %s alphabet.\n" ++ " Converting %c to %c.\n", ++ c, ++ alph_name(fasta_reader->alphabet), ++ c, ++ raw_sequence[i] ++ ); ++ } ++ ++seq_index; ++ } ++ } ++ if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) { ++ break; ++ } ++ } ++ ++ raw_sequence[seq_index] = '\0'; ++ return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file); ++} ++ + /****************************************************************************** +- * Fills in the next data block for the sequence. +- * During the first call for the sequence it fills in the full data block. +- * On successive calls, shifts the sequence in the block down one position +- * and reads one more character. ++ * Populates the data block for the with the next block of sequence. ++ * ++ * During the first call for the sequence it fills in a buffer from a file, ++ * The sequence pointer in the data block is set to point at the start of the buffer. ++ * On successive calls, the sequence pointer in the block is shifted down one position ++ * in the buffer. When the end of the buffer is reached, it is filled again from the file. + * + * Returns TRUE if it was able to completely fill the block, FALSE if + * the next sequence or EOF was reached before the block was filled. +--- a/src/seq-reader-from-fasta.h ++++ b/src/seq-reader-from-fasta.h +@@ -37,5 +37,30 @@ + int * end_ptr // end position of sequence (chr:\d+-(\d+)) + ); + ++/**************************************************************************** ++ * Read raw sequence until a new sequence is encountered or too many letters ++ * are read. ++ * ++ * Return: Was the sequence read completely? ++ ****************************************************************************/ ++BOOLEAN_T read_raw_sequence_from_reader( ++ DATA_BLOCK_READER_T *fasta_reader, // Sequence source ++ unsigned int max_chars, // Maximum chars in raw_sequence. ++ char* raw_sequence // Pre-allocated sequence. ++); ++ ++/**************************************************************************** ++ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder ++ * and copy them in to the raw sequence in the SEQ_T object starting at the ++ * given buffer offset. ++ ****************************************************************************/ ++void read_one_fasta_segment_from_reader( ++ DATA_BLOCK_READER_T *reader, ++ size_t max_size, ++ size_t offset, ++ SEQ_T *sequence ++); ++ ++ + size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader); + #endif diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch new file mode 100644 index 000000000000..498d1df7b664 --- /dev/null +++ b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch @@ -0,0 +1,54 @@ +--- a/doc/release-notes.html ++++ b/doc/release-notes.html +@@ -15,6 +15,21 @@ + </div> + <h2>MEME Suite Release Notes</h2> + <hr> ++ <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b> ++ <ul> ++ <li> ++ <b>Bug fixes</b> ++ <ul> ++ <li> ++ Fixed bug in handling of RNA-like custom alphabets. ++ </li> ++ <li> ++ Fixed bug in MAST -comp option. ++ </li> ++ </ul ++ </li> ++ </ul> ++ <hr> + <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b> + <ul> + <li> +--- a/src/alph-in.c ++++ b/src/alph-in.c +@@ -1044,7 +1044,7 @@ + lookup[0] = sym->complement; + comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup); + } +- if (comp1 != comp2) { ++ if (comp1 && (comp1 != comp2)) { + add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, + "not like %s alphabet as %c complement rules are incorrect", + ext_name, req_syms[i])); +--- a/src/mast-util.c ++++ b/src/mast-util.c +@@ -740,14 +740,14 @@ + + // create the frequency array + alph = xlate ? xlate_dest_alph(xlate) : alph; +- freq = allocate_array(alph_size_core(alph)); ++ freq = allocate_array(alph_size_full(alph)); + init_array(0, freq); + + // count the number of letters of each type + if (xlate) { + for (n=0; sequence[n]; n++) { + i = xlate_index(xlate, false, sequence+n); +- if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq); ++ if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq); + } + } else { + for (n=0; sequence[n]; n++) { diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild new file mode 100644 index 000000000000..0f7d25b43368 --- /dev/null +++ b/sci-biology/meme/meme-4.11.2_p2.ebuild @@ -0,0 +1,109 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools perl-functions python-single-r1 versionator + +MY_PV=$(get_version_component_range 1-3) +MY_P=${PN}_${MY_PV} + +DESCRIPTION="The MEME/MAST system - Motif discovery and search" +HOMEPAGE="http://meme-suite.org/tools/meme" +SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz" + +LICENSE="meme" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples mpi" + +RDEPEND=" + ${PYTHON_DEPS} + app-shells/tcsh + dev-libs/libxml2:2 + dev-libs/libxslt + sys-libs/zlib + app-text/ghostscript-gpl + media-gfx/imagemagick + dev-lang/perl:= + dev-perl/HTML-Parser + dev-perl/HTML-Template + dev-perl/Log-Log4perl + dev-perl/Math-CDF + dev-perl/XML-Compile-SOAP + dev-perl/XML-Compile-WSDL11 + dev-perl/XML-Parser + dev-perl/XML-Simple + virtual/perl-Data-Dumper + virtual/perl-Exporter + virtual/perl-File-Path + virtual/perl-File-Spec + virtual/perl-File-Temp + virtual/perl-Getopt-Long + virtual/perl-Scalar-List-Utils + virtual/perl-Time-HiRes + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND}" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch + "${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch + "${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch +) + +pkg_setup() { + python-single-r1_pkg_setup + perl_set_version +} + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --sysconfdir="${EPREFIX}"/etc/${PN} \ + --with-logs="${EPREFIX}"/var/log/${PN} \ + --with-perl=perl \ + --with-convert=convert \ + --with-gs=gs \ + --disable-build-libxml2 \ + --disable-build-libxslt \ + $(use_enable debug) \ + $(use_enable doc) \ + $(use_enable examples) \ + $(use_enable !mpi serial) \ + --with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \ + PYTHON="${EPYTHON}" + + # delete bundled libs, just to be sure. These need + # to be removed after econf, else AC_OUTPUT will fail + rm -r src/{libxml2,lib{,e}xslt} || die +} + +src_test() { + # bug #297070 + emake -j1 test +} + +src_install() { + default + docompress -x /usr/share/doc/${PF}/examples + + # prefix all binaries with 'meme-', in order + # to prevent collisions, bug 455010 + cd "${ED%/}"/usr/bin/ || die + local i + for i in *; do + if [[ $i != meme-* ]]; then + mv {,meme-}"${i}" || die + fi + done + + keepdir /var/log/meme +} diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/meme/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml new file mode 100644 index 000000000000..7a808874b6e6 --- /dev/null +++ b/sci-biology/metadata.xml @@ -0,0 +1,46 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<catmetadata> + <longdescription lang="en"> + The sci-biology category contains software that can be used + in biological and related scientific environments. + </longdescription> + <longdescription lang="de"> + Die Kategorie sci-biology enthält Software, die in biologischen + und verwandten wissenschaftlichen Umgebungen genutzt werden kann. + </longdescription> + <longdescription lang="es"> + La categorÃa sci-biology contiene programas que pueden ser utilizados en + entornos relacionados con la biologÃa. + </longdescription> + <longdescription lang="ja"> + sci-biologyカテゴリーã«ã¯ç”Ÿç‰©å¦ã®ç§‘å¦çš„ãªåˆ†é‡Žã«åˆ©ç”¨ã•ã‚Œã‚‹ + ソフトウェアãŒå«ã¾ã‚Œã¦ã„ã¾ã™ã€‚ + </longdescription> + <longdescription lang="nl"> + De sci-biology categorie bevat software, die in biologische en gerelateerde + wetenschappelijke omgevingen gebruikt kan worden. + </longdescription> + <longdescription lang="fr"> + La catégorie sci-biology contient des logiciels pour les sciences + biologiques et les disciplines connexes. + </longdescription> + <longdescription lang="vi"> + Nhóm sci-biology chứa các phần má»m sinh há»c và liên quan đến khoa há»c. + </longdescription> + <longdescription lang="sk"> + Kategória sci-biology obsahuje programy, ktoré sa použÃvajú pri + biologickom výskume. + </longdescription> + <longdescription lang="it"> + La categoria sci-biology contiene programmi per la biologia. + </longdescription> + <longdescription lang="pt"> + A categoria sci-biology contém programas que podem ser usados + em ambientes relacionados a biologia. + </longdescription> + <longdescription lang="pl"> + Kategoria sci-biology zawiera programy naukowe zwiÄ…zane z biologiÄ…. + </longdescription> +</catmetadata> + diff --git a/sci-biology/mira/Manifest 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ddd76e13a8cc27331d4352c7c3206fb96e29de7a4ff4fc47f4f7cd1f3cc2fd4b53947476d320397f87d4f5273754e78cdf300719575fdf3e04669e374d7e3c02 WHIRLPOOL 8298602a4f9da18ba845b60d24b787b2727adce4057db6b91c61dc783b9f0493540e17255f43a233f37ddedf74b96aec4c1119ac14d65ff6f12404879dbc034e +MISC metadata.xml 355 SHA256 516431894fbce903b3fe5539ea04820656e23c48dcd642e808a1af66ee8a23a6 SHA512 9d9037805b94622cb468553fa27c948de2849ac4c6dc1eafae8c3261554b5e97b631fe77e4e589eff613822d316b2843bcab0c47547b202651c8a804a516554e WHIRLPOOL ae8d0b1704c5d654d5669cfdea0ac0e7c14831c833ac00aa6d647f3ab523520d164dc42e8774ce7947a751f0b5da3f590f43826331bc9aafc914f49de913ce90 diff --git a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch new file mode 100644 index 000000000000..50f83c9021dc --- /dev/null +++ b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch @@ -0,0 +1,22 @@ +ax_boost_regex.m4 | 4 ++-- +1 file changed, 2 insertions(+), 2 deletions(-) + +--- mira-4.0.2/m4/ax_boost_regex.m4 ++++ mira-4.0.2/m4/ax_boost_regex.m4 +@@ -78,14 +78,14 @@ + for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + if test "x$link_regex" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + fi diff --git a/sci-biology/mira/files/mira-4.0.2-cmath.patch b/sci-biology/mira/files/mira-4.0.2-cmath.patch new file mode 100644 index 000000000000..a4a020177af7 --- /dev/null +++ b/sci-biology/mira/files/mira-4.0.2-cmath.patch @@ -0,0 +1,14 @@ +--- mira-4.0.2/src/mira/ads.C ++++ mira-4.0.2/src/mira/ads.C +@@ -31,10 +31,11 @@ + * Routines for computing scores and some other classification number are + * provided, too. + * + */ + ++#include <cmath> + + #include "ads.H" + + #include "errorhandling/errorhandling.H" + #include "util/dptools.H" diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch new file mode 100644 index 000000000000..78e7168cb49d --- /dev/null +++ b/sci-biology/mira/files/mira-4.0.2-cout.patch @@ -0,0 +1,27 @@ + src/progs/quirks.C | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/progs/quirks.C b/src/progs/quirks.C +index 47e5ee8..060b6f3 100644 +--- a/src/progs/quirks.C ++++ b/src/progs/quirks.C +@@ -25,6 +25,8 @@ + + #include <boost/filesystem.hpp> + ++#include <iostream> ++ + // make the "tcmalloc: large alloc" messages from TCMallom disappear + // by setting the reporting environment variable to a very large value + // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 +--- a/src/mira/parameters.C ++++ b/src/mira/parameters.C +@@ -2222,7 +2222,7 @@ + MIRANOTIFY(Notify::FATAL, "File not found: " << pfile); + } + +- parse(fin, Pv, nullptr); ++ parse(fin, Pv, false); + + fin.close(); + diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml new file mode 100644 index 000000000000..0704cef4806d --- /dev/null +++ b/sci-biology/mira/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">mira-assembler</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild new file mode 100644 index 000000000000..fd95fbfb2a78 --- /dev/null +++ b/sci-biology/mira/mira-4.0.2.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MIRA_3RDPARTY_PV="06-07-2012" +MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) + +inherit autotools eutils multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI=" + https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" +# https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 +# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +S="${WORKDIR}"/"${PN}"-"${MY_PV}" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc" + +CDEPEND=" + dev-libs/boost[threads] + dev-util/google-perftools" +DEPEND="${CDEPEND} + sys-devel/flex + app-editors/vim-core + dev-libs/expat" +RDEPEND="${CDEPEND}" + +#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED +# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) +DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) + +PATCHES=( + "${FILESDIR}/${PN}-4.0.2-boost-1.50.patch" + "${FILESDIR}/${PN}-4.0.2-cout.patch" + "${FILESDIR}/${PN}-4.0.2-cmath.patch" +) + +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + + default + + sed \ + -e "s:-O[23]::g" \ + -e "s:-funroll-loops::g" \ + -i configure.ac || die + + eautoreconf + + # Remove C++ source files that upstream built with flex. + local f + local PREBUILT_CXX_LEXER_FILES=( + "${S}"/src/caf/caf_flexer.cc + "${S}"/src/io/exp_flexer.cc + "${S}"/src/mira/parameters_flexer.cc + ) + + for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do + if [[ -f ${f} ]] ; then + rm "${f}" || die "Failed to remove ${f}" + else + die "${f} not found" + fi + done +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-thread=boost_thread-mt +} + +#src_compile() { +# base_src_compile +# # TODO: resolve docbook incompatibility for building docs +# if use doc; then emake -C doc clean docs || die; fi +#} + +src_install() { + default + + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} + dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} +} + +pkg_postinst() { + einfo "Documentation is no longer built, you can find it at:" + einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" +} diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest new file mode 100644 index 000000000000..adaa18c65bc6 --- /dev/null +++ b/sci-biology/mosaik/Manifest @@ -0,0 +1,8 @@ +AUX mosaik-2.2.30-Wformat-security.patch 3296 SHA256 3c69765e3c1d4602dd279b256990ccbcd1208a522a3bcef4754ab22f1ff1e777 SHA512 e72fa7cac8798425ac1dd4d3358bfdff640cc831a01531749ee2fad99f8b53bd64e8c7fcdddce205e9f6dd312cc74376afcba395ab8d508d92416190b7eed1df WHIRLPOOL df27b653648d71ade5c576923b5e7d54b48bd7ab414506e50ab6883b9e7b86d96f210d0e7311245cc52a7a58be38d46c0fbf58f074851bdf448900558a7aebf2 +AUX mosaik-2.2.30-fix-build-system.patch 8056 SHA256 88bd8b4419e5780ceae38cdb37dd07cf7d03e0c64e10490139e8f5f4d65daec3 SHA512 ed4a6efd9fb2fabd6c24adaa5894fde80024d8ee930450711c07388b62969a41e801f052ee88d7890355f1ddfc5ef9fbb40bfdabfbfae364c64c673ce08958c6 WHIRLPOOL 3abb198b14ef31663768a721f51245f072fde58bb2394ba2e4c260b9f8dbe8c22b0ad08aac3895b297d7ccedd7bc84b4c206181bc51821883175887d9debddb7 +AUX mosaik-2.2.30-remove-platform-code.patch 399 SHA256 3793acf75b1f369c799189f50169df3d0334e443b86164dd67175561fa74ebb2 SHA512 4aec709660b41fb61bb9219a587255a5f416992a4478c2a7eb67374d1425f0a4e0b4d356827a9214e2f2718b635169c95d3288bf10388a74e50d498c39c2f259 WHIRLPOOL 89c63cac8369cc576e972292a1fa1a9eabda528afe6e37ce942ec0b73d93df4ce3683d7fb774d944cef898a6e9de8a73a8d512cbbf55917a86d75a8d4c43945a +DIST mosaik-2.2.30.tar.gz 4387062 SHA256 685dcc4cde1b56d19be37bfb238ae4cddeb25dced6da7b3880e68973957e940e SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10 WHIRLPOOL 493291cc94cc5f95f5f1f62c3208f1c8dbb8cb0efcf6a21cca3e3963228f02ab0e59f11e00d8a9724a99733ffd290bc979262c0e553a1ee55c1adc9c392c3813 +EBUILD mosaik-2.2.30.ebuild 1104 SHA256 ea37ecc77194c75ce01496b514aebc8e390fc7be4bfac5cc1909d51e873ade07 SHA512 34863af564b085b85d1670b9c20fdc8ca8c5367e210a041c81d2cb67e5380e91636620214ebe06c347cb0ac556581d304374e527738c36b01029cf38a4846a4b WHIRLPOOL 57644a9e561244ef72d917c5a92bf25a36702ba1b44fabdc028c47d8dad1340b4929977a81aef1df5e059a31c9db250f2d16e4b8a282f943d4f171037c57024a +MISC ChangeLog 3305 SHA256 b8b8b1113cbdaf2fea6ca9ab28f001062c1610f2cedc2c535060b48d73268692 SHA512 adf81c6674b28b48da41e77efe2863fc18206e3619ee5822fb4185054fb22344bdf7bcdb928377fb17a065ab65e0b6f5302027c20cbee03d020684a31a5eb175 WHIRLPOOL de1f72644cd4f32637610bf571787deeb07ec81008cbfc3fc54cdd46526802abb429c822d4688f81d6aabd317a8701255562894aef8957d11c987eeae95e80e4 +MISC ChangeLog-2015 856 SHA256 23a69346ec54793f927a44a2ae7e02651a39e3b9f7175a048421130459d89b27 SHA512 8f910c7484fb486a57de9cfd3905f7d7cbe99017ce4a8049380260b5f11b63af9b19f381cac56426af6e517218ba02f2fd58fe1cf4393a99d6ff668d8e07b192 WHIRLPOOL af9db8386579802fdc37c68388e481af380764e57eb956adbf56f9e2b933787aeee08553e1a20f0fa2a0561bdeb6702179482ce53d113fafb95b8262b153de04 +MISC metadata.xml 414 SHA256 d17a60490c8a08b7e38bac22293e7163570929ae004eb017436017bee8b33b8e SHA512 2e6887226a0ac7457d1bbce1d76ac0953f0c1d5ff1d4261b7e11e4fa38803f01f8a67a285c2071671d58fcb8912ca8bb66bdfca93e2481be043ec5f2f2353c5b WHIRLPOOL 8e7ed6c4688ae4dbcaebba57db220aec9be52b058488ea4ea86a77b032ece920385736713edcc0db77e0b49c8174c86c352033694099f24604ccc05fa082a9b4 diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch b/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch new file mode 100644 index 000000000000..9f7271860229 --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch @@ -0,0 +1,84 @@ +- Fix incorrect printf format specifier (-Wformat) +* fann.c: In function ‘fann_print_connections’: +* fann.c:889:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] +* printf("L %3d / N %4d %s\n", layer_it - ann->first_layer, + +- Fix erroneous memset call +* md5.c: In function ‘MD5Final’: +* md5.c:152:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] +* memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ + +--- a/fann-2.1.0/fann.c ++++ b/fann-2.1.0/fann.c +@@ -886,7 +886,7 @@ + neurons[ann->connections[i] - ann->first_layer->first_neuron] = (char)('A' + value); + } + } +- printf("L %3d / N %4d %s\n", layer_it - ann->first_layer, ++ printf("L %3ld / N %4ld %s\n", layer_it - ann->first_layer, + neuron_it - ann->first_layer->first_neuron, neurons); + } + } +@@ -987,12 +987,12 @@ + { + if(ann->network_type == FANN_NETTYPE_SHORTCUT) + { +- printf(" Hidden layer :%4d neurons, 0 bias\n", ++ printf(" Hidden layer :%4ld neurons, 0 bias\n", + layer_it->last_neuron - layer_it->first_neuron); + } + else + { +- printf(" Hidden layer :%4d neurons, 1 bias\n", ++ printf(" Hidden layer :%4ld neurons, 1 bias\n", + layer_it->last_neuron - layer_it->first_neuron - 1); + } + } +--- a/fann-2.1.0/fann_io.c ++++ b/fann-2.1.0/fann_io.c +@@ -174,7 +174,7 @@ + #endif + + /* Save network parameters */ +- fprintf(conf, "num_layers=%u\n", ann->last_layer - ann->first_layer); ++ fprintf(conf, "num_layers=%ld\n", ann->last_layer - ann->first_layer); + fprintf(conf, "learning_rate=%f\n", ann->learning_rate); + fprintf(conf, "connection_rate=%f\n", ann->connection_rate); + fprintf(conf, "network_type=%u\n", ann->network_type); +@@ -236,7 +236,7 @@ + for(layer_it = ann->first_layer; layer_it != ann->last_layer; layer_it++) + { + /* the number of neurons in the layers (in the last layer, there is always one too many neurons, because of an unused bias) */ +- fprintf(conf, "%u ", layer_it->last_neuron - layer_it->first_neuron); ++ fprintf(conf, "%ld ", layer_it->last_neuron - layer_it->first_neuron); + } + fprintf(conf, "\n"); + +@@ -316,14 +316,14 @@ + if(save_as_fixed) + { + /* save the connection "(source weight) " */ +- fprintf(conf, "(%u, %d) ", ++ fprintf(conf, "(%ld, %d) ", + connected_neurons[i] - first_neuron, + (int) floor((weights[i] * fixed_multiplier) + 0.5)); + } + else + { + /* save the connection "(source weight) " */ +- fprintf(conf, "(%u, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]); ++ fprintf(conf, "(%ld, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]); + } + #else + /* save the connection "(source weight) " */ +--- a/CommonSource/Utilities/md5.c ++++ b/CommonSource/Utilities/md5.c +@@ -149,7 +149,7 @@ + MD5Transform(ctx->buf, (uint32 *) ctx->in); + byteReverse((unsigned char *) ctx->buf, 4); + memcpy(digest, ctx->buf, 16); +- memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ++ memset(ctx, 0, sizeof(*ctx)); /* In case it's sensitive */ + } + + diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch b/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch new file mode 100644 index 000000000000..00a9bec3ae4d --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch @@ -0,0 +1,226 @@ +- Make build system verbose by default, as required by Gentoo policy + See also: https://bugs.gentoo.org/show_bug.cgi?id=429308 +- Remove CFLAGS and CXXFLAGS defaults +- Fix order of flags and honour CPPFLAGS for LFS support + and LDFLAGS for --as-needed, respectively + +--- a/CommonSource/DataStructures/Makefile ++++ b/CommonSource/DataStructures/Makefile +@@ -22,7 +22,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/CommonSource/ExternalReadFormats/Makefile ++++ b/CommonSource/ExternalReadFormats/Makefile +@@ -22,7 +22,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/CommonSource/MosaikReadFormat/Makefile ++++ b/CommonSource/MosaikReadFormat/Makefile +@@ -22,7 +22,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/CommonSource/PairwiseAlignment/Makefile ++++ b/CommonSource/PairwiseAlignment/Makefile +@@ -26,11 +26,11 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(CBUILT_OBJECTS): $(CSOURCES) + @echo " * compiling" $(*F).c +- @$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c + + clean: + @echo "Cleaning up." +--- a/CommonSource/Utilities/Makefile ++++ b/CommonSource/Utilities/Makefile +@@ -48,11 +48,11 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(CBUILT_OBJECTS): $(CSOURCES) + @echo " * compiling" $(*F).c +- @$(CC) -c -o $@ $(*F).c -O3 -w -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CC) $(CFLAGS) $(CPPFLAGS) -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c + + clean: + @echo "Cleaning up." +--- a/fann-2.1.0/Makefile ++++ b/fann-2.1.0/Makefile +@@ -12,7 +12,7 @@ + + $(CBUILT_OBJECTS): $(CSOURCES) + @echo " * compiling" $(*F).c +- @$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) -I$(INCLUDES) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) -I$(INCLUDES) -c -o $@ $(*F).c + + clean: + @echo "Cleaning up." +--- a/Makefile ++++ b/Makefile +@@ -4,8 +4,8 @@ + # ========================== + + # define our object and binary directories +-export OBJ_DIR = ../obj +-export BIN_DIR = ../bin ++export OBJ_DIR = ./obj ++export BIN_DIR = ./bin + + # define our common source directories + export ASSEMBLY_DIR = CommonSource/AssemblyFormats +@@ -16,20 +16,6 @@ + export PAIRWISE_DIR = CommonSource/PairwiseAlignment + export UTILITIES_DIR = CommonSource/Utilities + +-# define some default flags +-FLAGS = -Wall -Wno-char-subscripts -ansi -O3 +-#FLAGS = -Wall -Wno-char-subscripts -ansi -g -D VERBOSE_DEBUG #gdb debugging +-#FLAGS = -Wall -Wno-char-subscripts -ansi -O3 -D VERBOSE_DEBUG #enables verbose debugging +-CFLAGS = +-CXXFLAGS = +-#CXXFLAGS = -ansi -pedantic -Wextra -Weffc++ +-CFLAGS += $(FLAGS) +-CXXFLAGS += $(FLAGS) +-export CFLAGS +-export CXXFLAGS +-#export LDFLAGS = -Wl +-export CXX ?= g++ +- + # define our platform + export BLD_PLATFORM ?= linux + include includes/$(BLD_PLATFORM).inc +--- a/MosaikAligner/Makefile ++++ b/MosaikAligner/Makefile +@@ -68,11 +68,11 @@ + + $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" +- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR) +--- a/MosaikBuild/Makefile ++++ b/MosaikBuild/Makefile +@@ -26,11 +26,11 @@ + + $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" +- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR) +--- a/MosaikJump/Makefile ++++ b/MosaikJump/Makefile +@@ -26,11 +26,11 @@ + + $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" +- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR) +--- a/MosaikText/Makefile ++++ b/MosaikText/Makefile +@@ -26,11 +26,11 @@ + + $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS) + @echo " * linking $(PROGRAM)" +- @$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS) + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR) +--- a/networkFile/retrainCode/attachXC/Makefile ++++ b/networkFile/retrainCode/attachXC/Makefile +@@ -3,12 +3,11 @@ + # (c) 2012 Wan-Ping Lee + # ========================== + +-FLAGS = -Wall -O3 + + + all: xc_pe.cpp xc_se.cpp +- @$(CXX) $(FLAGS) xc_pe.cpp -o xc_pe +- @$(CXX) $(FLAGS) xc_se.cpp -o xc_se ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_pe.cpp -o xc_pe ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_se.cpp -o xc_se + + .PHONY: all + +--- a/networkFile/retrainCode/trainNetwork/Makefile ++++ b/networkFile/retrainCode/trainNetwork/Makefile +@@ -5,8 +5,6 @@ + + OBJ_DIR = ./obj + +-FLAGS = -Wall -O3 +-CFLAGS = -O3 + FANN=../../../fann-2.1.0 + + SOURCES = sam_parser_float.cpp parameter_parser_float.cpp mq_train_float.cpp +@@ -15,12 +13,12 @@ + all: $(FANN)/floatfann.c $(SOURCES) + @test -d $(OBJ_DIR) || mkdir $(OBJ_DIR) + @echo " * compiling ......" +- @$(CC) $(CFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include +- @$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp +- @$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp +- @$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include + @echo " * linking ......" +- @$(CXX) $(FLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM) + + .PHONY: all + diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch b/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch new file mode 100644 index 000000000000..8573573ec125 --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch @@ -0,0 +1,10 @@ +- Remove macro for enabling large file support, this is better handled at an + ebuild level, where the LFS flags can be handled for multiple architectures +- Remove static flag, which is contrary to Gentoo policy + +--- a/includes/linux.inc ++++ b/includes/linux.inc +@@ -1,2 +1,2 @@ + # define our processor specific flags +-export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -static ++export PLATFORM_FLAGS = diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml new file mode 100644 index 000000000000..a3eca9b62b1c --- /dev/null +++ b/sci-biology/mosaik/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">mosaik-aligner</remote-id> + <remote-id type="github">wanpinglee/MOSAIK</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild new file mode 100644 index 000000000000..45633c47dab5 --- /dev/null +++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs vcs-snapshot + +DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies" +HOMEPAGE="https://github.com/wanpinglee/MOSAIK" +SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/${P}/src" + +PATCHES=( + "${FILESDIR}/${P}-remove-platform-code.patch" + "${FILESDIR}/${P}-fix-build-system.patch" + "${FILESDIR}/${P}-Wformat-security.patch" +) + +src_configure() { + # readd default warning flags from build system + append-flags -Wall -Wno-char-subscripts + append-lfs-flags + export BLD_PLATFORM=linux +} + +src_compile() { + emake \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin bin/Mosaik* + + dodoc ../README + + insinto /usr/share/${PN}/examples + doins -r ../demo/. +} diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest new file mode 100644 index 000000000000..c6d74e207412 --- /dev/null +++ b/sci-biology/mothur/Manifest @@ -0,0 +1,7 @@ +AUX mothur-1.27.0-makefile.patch 1196 SHA256 970d789187d58081bda269a863d965c1601ee18e09c39aa6dcaba2ef0aa89f5a SHA512 8a78ddbc926d4e116deed440fda8431ccbca3299ac182fc84850259187dc130cc43fb6f23845d055d998293fa43f94cbe35930242c5f6aa049f8275ad3e42adf WHIRLPOOL c0ae488479f430f212ff2158b74aa61ef9547b865be1db7ca3b546edf48907aa9aead69acfbc02c35b7d675209ac8f7d267a8f9a98ff167a0f73d0fc2efdd6ea +AUX mothur-1.27.0-overflows.patch 4894 SHA256 7b1f25400aa8f78ef55bcbd7d613eb877ce2774fc2e9492b6f9c544266661b5b SHA512 aa392b2060cecc38006a7ac50aaa8e4249a020029234ac2abdc33441b12a09faabb0335144ff4d888e55a1da1838a45347981f49f6658f3546a54a30b5e2133a WHIRLPOOL 7f0f8089b938c6a30ee13e217e21a4628ca56490aba36e7b6b14657ec70f3ba043243c80088be6b3e3d145835d4c3e3e3ee68d073f6556383a06e018f0cd716f +DIST mothur-1.27.0.zip 7095054 SHA256 7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 WHIRLPOOL 32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152b7777fcd09b3f9fb3bf60c7dd92d043a4bf361 +EBUILD mothur-1.27.0-r1.ebuild 881 SHA256 f485ea8a591e1fe7f1f121dda9b0dd8c58d301e86f947f8fe5cf98eb07ee2b8b SHA512 6f2fcb2d296ef3ef33786b579106f14ee0dfe05a50b53f5e0225c477598da1171cbd88e84f0fc7df5a973c221319a2fa23fb5cbddb339e7ede4e54b34b223be2 WHIRLPOOL 3a0a4e95ca0a7cc73e035f975d369b07ca5a5f75beea46f195856ee66cd64ac066606c4212f6676ecaac5b25182e4ce3fb2c3e3db90175de446165acc2522bdd +MISC ChangeLog 2910 SHA256 d1271431f72a4b8d1d9fd37fdb2cafa07b05167a80f67859740b2b547e540307 SHA512 f52727a3fb8ac2b61d833e4484aa7b597c4e1ee521d816403a98d86a2256968034ef4034cd61f1221d5745d5ca5aca9a4b398d56848d262084be99473f8c1a7d WHIRLPOOL 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file mode 100644 index 000000000000..52a02585df14 --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch @@ -0,0 +1,52 @@ + makefile | 14 ++++++-------- + 1 files changed, 6 insertions(+), 8 deletions(-) + +diff --git a/makefile b/makefile +index db7c904..109488f 100644 +--- a/makefile ++++ b/makefile +@@ -10,18 +10,18 @@ + # + + USEMPI ?= no +-64BIT_VERSION ?= yes ++64BIT_VERSION ?= no + USEREADLINE ?= yes + CYGWIN_BUILD ?= no + USECOMPRESSION ?= no + MOTHUR_FILES="\"Enter_your_default_path_here\"" + RELEASE_DATE = "\"8/8/2012\"" + VERSION = "\"1.27.0\"" +-FORTAN_COMPILER = gfortran +-FORTRAN_FLAGS = ++FORTAN_COMPILER = ${FC} ++FORTRAN_FLAGS = ${FCFLAGS} + + # Optimize to level 3: +-CXXFLAGS += -O3 ++#CXXFLAGS += -O3 + + ifeq ($(strip $(64BIT_VERSION)),yes) + #if you are using centos uncomment the following lines +@@ -69,7 +69,7 @@ endif + + + ifeq ($(strip $(USEMPI)),yes) +- CXX = mpic++ ++# CXX = mpic++ + CXXFLAGS += -DUSE_MPI + endif + +@@ -95,11 +95,9 @@ OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) + OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) + OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f)) + +-mothur : fortranSource $(OBJECTS) uchime ++mothur : fortranSource $(OBJECTS) + $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) + +- strip mothur +- + uchime: + cd uchime_src && ./mk && mv uchime .. && cd .. + diff --git a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch new file mode 100644 index 000000000000..0b612cf7b529 --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch @@ -0,0 +1,93 @@ + chimerauchimecommand.cpp | 2 +- + clearcutcommand.cpp | 32 ++++++++++++++++---------------- + 2 files changed, 17 insertions(+), 17 deletions(-) + +diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp +index bd31c19..2070840 100644 +--- a/chimerauchimecommand.cpp ++++ b/chimerauchimecommand.cpp +@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc + } + + if (ucl) { +- char* tempucl = new char[5]; ++ char* tempucl = new char[6]; + strcpy(tempucl, "--ucl"); + cPara.push_back(tempucl); + } +diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp +index 6a0eb25..2e8164e 100644 +--- a/clearcutcommand.cpp ++++ b/clearcutcommand.cpp +@@ -269,35 +269,35 @@ int ClearcutCommand::execute() { + + vector<char*> cPara; + +- char* tempClearcut = new char[8]; ++ char* tempClearcut = new char[16]; + strcpy(tempClearcut, "clearcut"); + cPara.push_back(tempClearcut); + + //you gave us a distance matrix +- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); } ++ if (phylipfile != "") { char* temp = new char[16]; strcpy(temp, "--distance"); cPara.push_back(temp); } + + //you gave us a fastafile +- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); } ++ if (fastafile != "") { char* temp = new char[16]; strcpy(temp, "--alignment"); cPara.push_back(temp); } + +- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); } +- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); } +- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); } ++ if (version) { char* temp = new char[16]; strcpy(temp, "--version"); cPara.push_back(temp); } ++ if (verbose) { char* temp = new char[16]; strcpy(temp, "--verbose"); cPara.push_back(temp); } ++ if (quiet) { char* temp = new char[16]; strcpy(temp, "--quiet"); cPara.push_back(temp); } + if (seed != "*") { + string tempSeed = "--seed=" + seed; + char* temp = new char[tempSeed.length()]; + strcpy(temp, tempSeed.c_str()); + cPara.push_back(temp); + } +- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); } +- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } +- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } ++ if (norandom) { char* temp = new char[16]; strcpy(temp, "--norandom"); cPara.push_back(temp); } ++ if (shuffle) { char* temp = new char[16]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } ++ if (neighbor) { char* temp = new char[16]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } + + string tempIn = "--in=" + inputFile; + char* tempI = new char[tempIn.length()]; + strcpy(tempI, tempIn.c_str()); + cPara.push_back(tempI); + +- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); } ++ if (stdoutWanted) { char* temp = new char[16]; strcpy(temp, "--stdout"); cPara.push_back(temp); } + else{ + string tempOut = "--out=" + outputName; + +@@ -306,10 +306,10 @@ int ClearcutCommand::execute() { + cPara.push_back(temp); + } + +- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); } +- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); } +- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); } +- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); } ++ if (DNA) { char* temp = new char[16]; strcpy(temp, "--DNA"); cPara.push_back(temp); } ++ if (protein) { char* temp = new char[16]; strcpy(temp, "--protein"); cPara.push_back(temp); } ++ if (jukes) { char* temp = new char[16]; strcpy(temp, "--jukes"); cPara.push_back(temp); } ++ if (kimura) { char* temp = new char[16]; strcpy(temp, "--kimura"); cPara.push_back(temp); } + if (matrixout != "") { + string tempMatrix = "--matrixout=" + outputDir + matrixout; + char* temp = new char[tempMatrix.length()]; +@@ -326,8 +326,8 @@ int ClearcutCommand::execute() { + cPara.push_back(temp); + } + +- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); } +- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); } ++ if (expblen) { char* temp = new char[16]; strcpy(temp, "--expblen"); cPara.push_back(temp); } ++ if (expdist) { char* temp = new char[16]; strcpy(temp, "--expdist"); cPara.push_back(temp); } + + char** clearcutParameters; + clearcutParameters = new char*[cPara.size()]; diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/mothur/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild new file mode 100644 index 000000000000..d12d3c9b4399 --- /dev/null +++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 toolchain-funcs + +DESCRIPTION="A suite of algorithms for ecological bioinformatics" +HOMEPAGE="http://www.mothur.org/" +SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="mpi +readline" +KEYWORDS="amd64 x86" + +RDEPEND=" + sci-biology/uchime + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + app-arch/unzip" + +S=${WORKDIR}/Mothur.source + +pkg_setup() { + fortran-2_pkg_setup + use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX) + use amd64 && append-cppflags -DBIT_VERSION +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-overflows.patch +} + +src_compile() { + emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest new file mode 100644 index 000000000000..4a7a73623659 --- /dev/null +++ b/sci-biology/mrbayes/Manifest @@ -0,0 +1,7 @@ +AUX mb_readline_312.patch 1108 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22 SHA512 0a169b8560853dbff87c983bf8220384dcf22f53106ce5711bf3b1fc76d8a9adbf1860618176dde65a8657abe3ad888521bf5485fc00d4014adf1acb7ba3f114 WHIRLPOOL 925581e97278d36cdbfa4c53ab47a331640cf0d57c912eee7567d28805875a15e677a283f7a941c851783057cd606165ebccd6360e4f705eae53b2bf8df0fa89 +DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 WHIRLPOOL 45c9750a1e3e3ac85a1085bcaf8fc5c108b730a3dfa2f9e8d81cea8720bd6f02815c3145c19ee6c369a43f4565c2b234ec81cd5721672abded17186264de2e3f +EBUILD mrbayes-3.1.2-r1.ebuild 1008 SHA256 4ed3c0c65258e1bdabac5a3a461660862faecd809a0d7d4fb7eea219c0b0eb6d SHA512 5fcbdd396c7b035ecc0b596a9866fdc3544cf8993fd60efa0a5ab41f7cd4271c437626e3c131d9d07759cecef3cb8700a0b5b761ec87cbcbf12b9d206543f918 WHIRLPOOL 65d442f033f1eea5e6ee4dc89f9514e6e9738996b8da169c850b31baa8a5b8a09aa133d29456768190e9a6d838a944056e962ae7c454e7fa021aee42e9a15404 +EBUILD mrbayes-3.1.2-r2.ebuild 1347 SHA256 ace0ceab6ce36430d74c70d4bae913053aa13978f51c0b148b8f391caa587dfa SHA512 c8655ecaf9933a963b072a242e44c156f89c635fae00fa135262911e2588beb623764a92634c27a16dcdac4fb70c16b88a428aa154a56ea816fd9b9ff2418037 WHIRLPOOL 57a34def5ab5c89fa72153b5e93b1d16cacafd0ad2404dfdf47aa2d3ba91627eea0cc9a0bfac83a17202494fdfbb26b05482fc036773b0222f9de5909e713140 +MISC ChangeLog 2658 SHA256 dcb2547bd0d07004b50e6e8a8ef179e3ce5e9c07b2f91c4783394d33d7f93112 SHA512 1be3d35c10b13c4f0fbd7f38a41678001133e58eef4436efbb6083002bd0a695f4823647bb4553142ddf182d83f60f49e0528614a5ff1fd929ba1fbc9feb12aa WHIRLPOOL 54940fc6251c4cebd53f07623a3dc0213de8c9d948b6922e1a2918e4615857037089e7a3605cb55dad7104a32d807bc56ba3acbd52005217c67ba3a280b5ada3 +MISC ChangeLog-2015 3659 SHA256 624f09b69c5d303e7dbcceae7cf41a0a0961a8affdea23e3a70ee4e5c10142af SHA512 68cb1b6c4177abf3ed1dd339edbff99c87bb70e16d637588f9d76ef798ca501a148a0a6b751c3fcc5df9b1b28305379a3b4e157973e6bbbce7bb10eb5c9dbdf3 WHIRLPOOL bd446c6d7ee8dba16098c97f203a52450ef924862838ffad53b75db387a8547c258f43dc65a81fc576699d5c99239736f7837e46518c5c7e8a656119111fd1b4 +MISC metadata.xml 916 SHA256 44be6660a7e4d632ae6a0bc88f8a4850beb6865e21634a75a0746a0e67849bb9 SHA512 ab6be2e4111088bc13e6da5f65d11437dc05dbcdeab83e5d3899b913ff9ad3dc1f22ec81f2fe73f60bf991d01f0a8691eaa124ba24bd7ebb17d995fdd271bfef WHIRLPOOL 208fdc5fc49d67b4124d4dfcf7ae678c5646f67734c543e7c922b3bde17568815caad894df954ce4f1b549118b552a60524a7871cd539b32b3cba95aac4b5db3 diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch new file mode 100644 index 000000000000..2f8bab1e7665 --- /dev/null +++ b/sci-biology/mrbayes/files/mb_readline_312.patch @@ -0,0 +1,37 @@ +Index: Makefile +=================================================================== +RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v +retrieving revision 3.23 +retrieving revision 3.24 +diff -U2 -r3.23 -r3.24 +--- Makefile 22 Dec 2005 16:13:06 -0000 3.23 ++++ Makefile 3 Jan 2006 16:43:13 -0000 3.24 +@@ -50,4 +50,5 @@ + ifeq ($(strip $(USEREADLINE)),yes) + CFLAGS += -DUSE_READLINE ++# CFLAGS += -DCOMPLETIONMATCHES + LIBS += -lncurses -lreadline + endif +Index: bayes.c +=================================================================== +RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v +retrieving revision 3.39 +retrieving revision 3.40 +diff -U2 -r3.39 -r3.40 +--- bayes.c 23 Dec 2005 16:26:28 -0000 3.39 ++++ bayes.c 3 Jan 2006 16:43:13 -0000 3.40 +@@ -382,9 +382,11 @@ + char **readline_completion(const char *text, int start, int stop) { + char **matches = (char **) NULL; +- ++ ++#ifdef COMPLETIONMATCHES + if(start == 0) +- matches = rl_completion_matches (text, command_generator); ++ matches = rl_completion_matches (text, command_generator); ++#endif + +- return (matches); ++ return (matches); + } + #endif diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml new file mode 100644 index 000000000000..ca6afd95a12e --- /dev/null +++ b/sci-biology/mrbayes/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> +MrBayes is a program for the Bayesian estimation of phylogeny. +Bayesian inference of phylogeny is based upon a quantity called the +posterior probability distribution of trees, which is the probability of a +tree conditioned on the observations. The conditioning is accomplished using +Bayes's theorem. The posterior probability distribution of trees is +impossible to calculate analytically; instead, MrBayes uses a simulation +technique called Markov chain Monte Carlo (or MCMC) to approximate the +posterior probabilities of trees. +</longdescription> + <upstream> + <remote-id type="sourceforge">mrbayes</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild new file mode 100644 index 000000000000..b67b4b228f9b --- /dev/null +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Bayesian Inference of Phylogeny" +HOMEPAGE="http://mrbayes.csit.fsu.edu/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="debug mpi readline" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND=" + sys-libs/ncurses + mpi? ( virtual/mpi ) + readline? ( sys-libs/readline:0 )" +RDEPEND="${DEPEND}" + +src_prepare() { + use readline && epatch "${FILESDIR}"/mb_readline_312.patch + sed -e 's:-ggdb::g' -i Makefile || die +} + +src_compile() { + local myconf mycc + + if use mpi; then + mycc=mpicc + else + mycc=$(tc-getCC) + fi + + use mpi && myconf="MPI=yes" + use readline || myconf="${myconf} USEREADLINE=no" + use debug && myconf="${myconf} DEBUG=yes" + emake \ + OPTFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + CC=${mycc} \ + ${myconf} +} + +src_install() { + dobin mb + insinto /usr/share/${PN} + doins *.nex +} diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild new file mode 100644 index 000000000000..ebe9926212c9 --- /dev/null +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Bayesian Inference of Phylogeny" +HOMEPAGE="http://mrbayes.csit.fsu.edu/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="debug mpi readline" + +DEPEND=" + sys-libs/ncurses:0= + mpi? ( virtual/mpi ) + readline? ( sys-libs/readline:0= )" +RDEPEND="${DEPEND}" + +src_prepare() { + if use mpi; then + sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support." + fi + if ! use readline; then + sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \ + -i Makefile || die "Patching readline support." + else + # Only needed for OSX with an old (4.x) version of + # libreadline, but it doesn't hurt for other distributions. + epatch "${FILESDIR}"/mb_readline_312.patch + fi + sed -e 's:-ggdb::g' -i Makefile || die +} + +src_compile() { + local myconf mycc + + if use mpi; then + mycc=mpicc + else + mycc=$(tc-getCC) + fi + + use mpi && myconf="MPI=yes" + use readline || myconf="${myconf} USEREADLINE=no" + use debug && myconf="${myconf} DEBUG=yes" + emake \ + OPTFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + CC=${mycc} \ + ${myconf} +} + +src_install() { + dobin mb + insinto /usr/share/${PN} + doins *.nex +} diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest new file mode 100644 index 000000000000..e1ee929f6519 --- /dev/null +++ b/sci-biology/mummer/Manifest @@ -0,0 +1,8 @@ +AUX mummer-3.23-fix-build-system.patch 10130 SHA256 4cb6a96d68713039b8edf796960bcd5adf00751869acbbe12b377f5cf1176b81 SHA512 4979c8ab1fde7a134e2feb5a758fbd1b9fe125e056e53f09ea620183d9b2492452cd8be473e474c8a88e4a25acbd7e20d401146c38cbedee564a03a601f92ca0 WHIRLPOOL 86d31520296191005c05b0f82a66ca05af91d5d7db75622faec6c26b717b603cd24f7fd171c1dda4619efee4b45006dafe7d41f488dcf63aa714fc7ce443c2e4 +AUX mummer-3.23-fix-c++-qa.patch 2615 SHA256 99acb89564439528b30f64448c193cd8302e58c7503b5d87074301bf2e712e42 SHA512 ca1a8156ecac367817f4678ed9fd0dd7e5f31cce0d8d167dd9245ea1e2ad4b4acad254277483f99764891a0cbad8ca6f879acc731b8e3e306e5644739c0f82d2 WHIRLPOOL a72fb08be411694fa5050628a1825050fe364243db8ee1d774e8ac3a7e02d0f8ad5937f607d314e4d84abf18481e2a25f52b8e2835385a077b48312bce792544 +AUX mummer-3.23-fix-shebangs.patch 2357 SHA256 1307243770f1af4aa508a00715d29b571b169807aa0102d8ec30af7becef335e SHA512 d0ac58170232244385328d3a23e6b8203593d32dda30d75915b4da8ad935fc1dc447b2a7c7d982b0a86c9fe4ca6f8c2031fe7f81af8a72bfba4d56ae6d246235 WHIRLPOOL 3c3fbbe2b99cda779283a9d9dc0b4b586c98dc1ba213be2c1007e9f170d80f72c4c253e599824aed2f8607c815f614619955f8b79d75778e9c34265f570f49c1 +DIST MUMmer3.23.tar.gz 3160143 SHA256 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 WHIRLPOOL 7471d20a88f5ddf510d1e4826480706a683f005f3bab21ebb19b1fcba2c8f431435cce27a1cdf98ece8d4bb4dafcc349362037f6d526db3f564b7c013c67e882 +EBUILD mummer-3.23.ebuild 1133 SHA256 da065cb1a4314c709fb6fcac8a2079dcfb31664cd7b3430e19071e609ec9d6f8 SHA512 a25b94cb5e7a8261178d0a503c33812f106dde277c94a8525a0a8fcd6c120ec6b0d5cb80f26f0710245f89251ad4ac6e4fe86af42f31b31f37ab9eca6afc3b79 WHIRLPOOL 205e432b5a3c915913f15ebbe2ee2710e85a54ff1967ad26a4459a4f8c599fd828abea6813439c61d5d5e71884dd09603693e3d8facb3028b56b6b2cf753dd08 +MISC ChangeLog 2614 SHA256 c419c030871bff1d34b413648db36e3d476ecda28b88cb145925695b144661da SHA512 11b57a837714ea4725b07e0d3b5e09c621c40d7a362705a346d2562868d525eec054ae74147d07095f3e0c19cf865295ba1938743b2ddceae4371644ff029f8b WHIRLPOOL 4bbe42eaf6eed492df2ab6d192d8e7c29fe78cad9648c9cca9c1266f3267349cb5dee61b755d6a8ffb6b6278ba956ce342b4a82cfa10fb6b2aa8092d08ac75c1 +MISC ChangeLog-2015 2204 SHA256 6ba244dff6d066d6365eb4eb986cbc76f93015f16de562b2cabcb6e07805ac8e SHA512 b5c4554ef2cdc436db529a2122558857549683c7742e8a47cc8fcf01e1aa833036d4f6797fd5e8dc2339a44052a20e075b2aacb9e991757271c63dbf7d6bf392 WHIRLPOOL f33a5caa560957d50597daf1ff5bdccfd122378e24e5288bc0d3b592ea30e970332eb67df76377fb7c2186a64a2ab441b3127e8b0a67babd7dfff2cdf9f26802 +MISC metadata.xml 347 SHA256 090b02afe3d221595404585ab81794b7200d2debc18bbd87778a420e2c93bd9b SHA512 7465b510db1cbf2b5853452e947585e6526068aaa0562b7e3ad415838d97ecf30cf32967997c16bab17ac9c41921c0f92dc2a9647fde402f448d6f6dc1d2244c WHIRLPOOL e02461914ac5c1b2607dd7429486e9e0a0ccfbce3cc7e1543af724dd57a43660a974b6050a797123be01eefea593a8ed8277a983dece07708914e3c2829c7e96 diff --git a/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch new file mode 100644 index 000000000000..b92f75c07719 --- /dev/null +++ b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch @@ -0,0 +1,397 @@ +Fix build system to restore some sanity + +--- a/Makefile ++++ b/Makefile +@@ -27,31 +27,27 @@ + + + TOP_DIR := $(CURDIR) +-BIN_DIR := $(TOP_DIR) +-AUX_BIN_DIR := $(TOP_DIR)/aux_bin ++ ++BIN_DIR = $(EPREFIX)/usr/bin ++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts ++AUX_BIN_DIR = $(EPREFIX)/usr/bin + + DOC_DIR := $(TOP_DIR)/docs + SCRIPT_DIR := $(TOP_DIR)/scripts + TIGR_SRC_DIR := $(TOP_DIR)/src/tigr + KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz + +-CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) +-CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) + SED := $(filter /%,$(shell /bin/sh -c 'type sed')) + CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) + PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +-AR := $(filter /%,$(shell /bin/sh -c 'type ar')) + +-CXXFLAGS = -O3 +-CFLAGS = -O3 +-LDFLAGS = + + FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog + + + + #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES +-export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS ++export BIN_DIR SCRIPT_DIR AUX_BIN_DIR + + + +@@ -114,15 +110,15 @@ + + + kurtz: +- cd $(KURTZ_SRC_DIR); $(MAKE) mummer ++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer + + + scripts: +- cd $(SCRIPT_DIR); $(MAKE) all ++ $(MAKE) -C $(SCRIPT_DIR) all + + + tigr: +- cd $(TIGR_SRC_DIR); $(MAKE) all ++ $(MAKE) -C $(TIGR_SRC_DIR) all + + + uninstall: clean +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,21 +1,10 @@ +-#-- Imported variables from top level makefile +-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS ++BIN_DIR = $(EPREFIX)/usr/bin ++SCRIPT_DIR = $(EPREFIX)/usr/share/mummer/scripts ++AUX_BIN_DIR = $(EPREFIX)/usr/bin + +-ifndef BIN_DIR +-BIN_DIR := $(CURDIR) +-endif +-ifndef AUX_BIN_DIR +-AUX_BIN_DIR := $(CURDIR) +-endif +-ifndef SCRIPT_DIR +-SCRIPT_DIR := $(CURDIR) +-endif +- +-SCRIPT_DIR := $(CURDIR) + SED := $(filter /%,$(shell /bin/sh -c 'type sed')) + CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) + PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +-VPATH := $(BIN_DIR) + + ALL := exact-tandems mapview mummerplot nucmer promer \ + run-mummer1 run-mummer3 nucmer2xfig dnadiff +@@ -39,58 +28,49 @@ + $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ +- exact-tandems.csh > $(BIN_DIR)/exact-tandems +- chmod 755 $(BIN_DIR)/exact-tandems ++ exact-tandems.csh > exact-tandems + + mapview: mapview.pl + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ +- mapview.pl > $(BIN_DIR)/mapview +- chmod 755 $(BIN_DIR)/mapview ++ mapview.pl > mapview + + mummerplot: mummerplot.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- mummerplot.pl > $(BIN_DIR)/mummerplot +- chmod 755 $(BIN_DIR)/mummerplot ++ mummerplot.pl > mummerplot + + dnadiff: dnadiff.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- dnadiff.pl > $(BIN_DIR)/dnadiff +- chmod 755 $(BIN_DIR)/dnadiff ++ dnadiff.pl > dnadiff + + nucmer: nucmer.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- nucmer.pl > $(BIN_DIR)/nucmer +- chmod 755 $(BIN_DIR)/nucmer ++ nucmer.pl > nucmer + + promer: promer.pl Foundation.pm + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ + -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ + -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- promer.pl > $(BIN_DIR)/promer +- chmod 755 $(BIN_DIR)/promer ++ promer.pl > promer + + run-mummer1: run-mummer1.csh + $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- run-mummer1.csh > $(BIN_DIR)/run-mummer1 +- chmod 755 $(BIN_DIR)/run-mummer1 ++ run-mummer1.csh > run-mummer1 + + run-mummer3: run-mummer3.csh + $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ + -e 's?__BIN_DIR?$(BIN_DIR)?g' \ +- run-mummer3.csh > $(BIN_DIR)/run-mummer3 +- chmod 755 $(BIN_DIR)/run-mummer3 ++ run-mummer3.csh > run-mummer3 + + nucmer2xfig: nucmer2xfig.pl + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ +- nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig +- chmod 755 $(BIN_DIR)/nucmer2xfig ++ nucmer2xfig.pl > nucmer2xfig +--- a/src/kurtz/libbasedir/Makefile ++++ b/src/kurtz/libbasedir/Makefile +@@ -5,8 +5,6 @@ + + SPLINTFLAGS=-f ../Splintoptions -DDEBUG + +-LD=$(CC) +- + ##CFLAGS=${DEFINECFLAGS} + + LIBBASE=libbase.a +@@ -24,14 +22,14 @@ + + + $(LIBBASE): $(LIBOBJECTS) +- ar sruv $@ $(LIBOBJECTS) ++ $(AR) sruv $@ $(LIBOBJECTS) + + + include Filegoals.mf + + + $(LIBBASEDBG): $(LIBDEBUGOBJECTS) +- ar sruv $@ $(LIBDEBUGOBJECTS) ++ $(AR) sruv $@ $(LIBDEBUGOBJECTS) + + + .PHONY:clean +--- a/src/kurtz/Makefile ++++ b/src/kurtz/Makefile +@@ -1,7 +1,7 @@ + all: +- cd libbasedir; $(MAKE) all +- cd streesrc; $(MAKE) all +- cd mm3src; $(MAKE) all ++ $(MAKE) -C libbasedir all ++ $(MAKE) -C streesrc all ++ $(MAKE) -C mm3src all + + clean: + rm -f *~ +@@ -10,11 +10,11 @@ + cd mm3src; $(MAKE) clean + + mummer: +- cd libbasedir; $(MAKE) libbase.a +- cd streesrc; $(MAKE) libstree.a +- cd mm3src; $(MAKE) mummer ++ $(MAKE) -C libbasedir libbase.a ++ $(MAKE) -C streesrc libstree.a ++ $(MAKE) -C mm3src mummer + + splintall: +- cd libbasedir; ${MAKE} splintall +- cd streesrc; ${MAKE} splintall +- cd mm3src; ${MAKE} splintall ++ $(MAKE) -C libbasedir splintall ++ $(MAKE) -C streesrc splintall ++ $(MAKE) -C mm3src splintall +--- a/src/kurtz/mm3src/Makefile ++++ b/src/kurtz/mm3src/Makefile +@@ -3,11 +3,7 @@ + + ##include ../Makedef + +-ifndef BIN_DIR +-BIN_DIR := $(CURDIR) +-endif +- +-VPATH := $(BIN_DIR) ++BIN_DIR = $(EPREFIX)/usr/bin + + ALL := maxmat3.x maxmat3.dbg.x + +@@ -15,11 +11,8 @@ + LIBSTREEDIR=../streesrc + INCLUDEDIR=-I${LIBBASEDIR} -I${LIBSTREEDIR} + +-override CFLAGS+=$(INCLUDEDIR) +-##CFLAGS=${DEFINECFLAGS} $(INCLUDEDIR) +-##LDFLAGS=${DEFINELDFLAGS} ++override CPPFLAGS+=$(INCLUDEDIR) + SPLINTFLAGS=${INCLUDEDIR} -f ../Splintoptions -DDEBUG +-LD=$(CC) + + LIBBASE=$(LIBBASEDIR)/libbase.a + LIBBASEDBG=$(LIBBASEDIR)/libbase.dbg.a +@@ -40,16 +33,16 @@ + all: $(ALL) + + mummer: $(MUM3OBJECTS) $(LIBSTREE) +- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ +- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ ++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ ++ -o $@ + + maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE) +- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ +- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ ++ $(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ ++ -o $@ + + maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG) +- $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ +- -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ ++ $(CC) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ ++ -lm -o $@ + + include Filegoals.mf + +--- a/src/kurtz/streesrc/Makefile ++++ b/src/kurtz/streesrc/Makefile +@@ -23,8 +23,6 @@ + + #-DSTARTFACTOR=0.5 + +-LD=${CC} +- + LIBBASE=${LIBBASEDIR}/libbase.a + LIBBASEDBG=${LIBBASEDIR}/libbase.dbg.a + +@@ -65,29 +63,29 @@ + include Filegoals.mf + + libstree.4.a: $(OBJECTS4) +- ar sruv $@ $(OBJECTS4) ++ $(AR) sruv $@ $(OBJECTS4) + + libstree.a: $(OBJECTS) +- ar sruv $@ $(OBJECTS) ++ $(AR) sruv $@ $(OBJECTS) + + libstree.dbg.4.a: $(DBGOBJECTS4) +- ar sruv $@ $(DBGOBJECTS4) ++ $(AR) sruv $@ $(DBGOBJECTS4) + + libstree.dbg.a: $(DBGOBJECTS) +- ar sruv $@ $(DBGOBJECTS) ++ $(AR) sruv $@ $(DBGOBJECTS) + + + stree.x: stree.o libstree.a +- $(LD) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@ ++ $(CC) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@ + + loc.x: loc.o libstree.a +- $(LD) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@ ++ $(CC) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@ + + stree.dbg.x: stree.dbg.o libstree.dbg.a +- $(LD) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ ++ $(CC) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ + + loc.dbg.x: loc.dbg.o libstree.dbg.a +- $(LD) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ ++ $(CC) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@ + + streeproto.h: $(PROTOFILES) Mkstreeproto.sh + @echo "make $@" +--- a/src/tigr/Makefile ++++ b/src/tigr/Makefile +@@ -1,20 +1,3 @@ +-#-- Imported variables from top level makefile +-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS +- +-ifndef BIN_DIR +-BIN_DIR := $(CURDIR) +-endif +-ifndef AUX_BIN_DIR +-AUX_BIN_DIR := $(CURDIR) +-endif +- +-OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@ +-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ +- chmod 755 $(BIN_DIR)/$@ +-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ +- chmod 755 $(AUX_BIN_DIR)/$@ +-VPATH := $(AUX_BIN_DIR):$(BIN_DIR) +- + ALL := annotate combineMUMs delta-filter gaps mgaps \ + postnuc postpro prenuc prepro repeat-match \ + show-aligns show-coords show-tiling show-snps \ +@@ -38,59 +21,22 @@ + + #-- not so PHONY rules --# + delta.o: delta.cc delta.hh +- $(OBJ_RULE) +- + tigrinc.o: tigrinc.cc tigrinc.hh +- $(OBJ_RULE) +- + sw_align.o: sw_align.cc sw_align.hh tigrinc.hh +- $(OBJ_RULE) +- + translate.o: translate.cc translate.hh +- $(OBJ_RULE) +- + + annotate: annotate.cc tigrinc.o +- $(BIN_RULE) +- + combineMUMs: combineMUMs.cc tigrinc.o +- $(BIN_RULE) +- + delta-filter: delta-filter.cc tigrinc.o delta.o +- $(BIN_RULE) +- + gaps: gaps.cc tigrinc.o +- $(BIN_RULE) +- + mgaps: mgaps.cc tigrinc.o +- $(BIN_RULE) +- + postnuc: postnuc.cc tigrinc.o sw_align.o +- $(AUX_BIN_RULE) +- + postpro: postpro.cc tigrinc.o sw_align.o translate.o +- $(AUX_BIN_RULE) +- + prenuc: prenuc.cc tigrinc.o +- $(AUX_BIN_RULE) +- + prepro: prepro.cc tigrinc.o translate.o +- $(AUX_BIN_RULE) +- + repeat-match: repeat-match.cc tigrinc.o +- $(BIN_RULE) +- + show-aligns: show-aligns.cc tigrinc.o translate.o delta.o +- $(BIN_RULE) +- + show-coords: show-coords.cc tigrinc.o delta.o +- $(BIN_RULE) +- + show-tiling: show-tiling.cc tigrinc.o delta.o +- $(BIN_RULE) +- + show-snps: show-snps.cc tigrinc.o translate.o delta.o +- $(BIN_RULE) +- + show-diff: show-diff.cc tigrinc.o delta.o +- $(BIN_RULE) diff --git a/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch b/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch new file mode 100644 index 000000000000..d6926c913d4a --- /dev/null +++ b/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch @@ -0,0 +1,83 @@ +--- a/src/kurtz/libbasedir/space.c ++++ b/src/kurtz/libbasedir/space.c +@@ -379,7 +379,7 @@ + } + if(numberofblocks > 0) + { +- fprintf(stderr,"space leak: number of blocks = %u\n",numberofblocks); ++ fprintf(stderr,"space leak: number of blocks = %lu\n",numberofblocks); + exit(EXIT_FAILURE); + } + free(blocks); +--- a/src/tigr/combineMUMs.cc ++++ b/src/tigr/combineMUMs.cc +@@ -106,7 +106,7 @@ + // This array [i] is the maximum number of errors allowed + // in a match between sequences of length i , which is + // i * MAXERROR_RATE . +-char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; ++const char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; + // Name of file to write gaps listing with # errors in each gap + int Fill_Ct = 0; + // Number of non-acgt bases in ref sequence +@@ -132,7 +132,7 @@ + // The query sequence + long int Query_Len; + // The length of the query sequence +-char * Query_Suffix = "Query"; ++const char * Query_Suffix = "Query"; + // Suffix for query tag + char * Ref = NULL; + // The reference sequence +@@ -142,7 +142,7 @@ + // The length of the reference sequence + long int Ref_Size; + // The size of the reference sequence buffer +-char * Ref_Suffix = "Ref"; ++const char * Ref_Suffix = "Ref"; + // Suffix for reference tag + int Show_Differences = FALSE; + // If TRUE then show differences in all alignments +--- a/src/tigr/mgaps.cc ++++ b/src/tigr/mgaps.cc +@@ -64,9 +64,9 @@ + static void Parse_Command_Line
+ (int argc, char * argv []);
+ static void Process_Matches
+- (Match_t * A, int N, char * label);
++ (Match_t * A, int N, const char * label);
+ static int Process_Cluster
+- (Match_t * A, int N, char * label);
++ (Match_t * A, int N, const char * label);
+ static void Union
+ (int a, int b);
+ static void Usage
+@@ -438,7 +438,7 @@ +
+
+ static int Process_Cluster
+- (Match_t * A, int N, char * label)
++ (Match_t * A, int N, const char * label)
+
+ // Process the cluster of matches in A [0 .. (N - 1)] and output them
+ // after a line containing label . Return the number of clusters
+@@ -552,7 +552,7 @@ +
+
+ static void Process_Matches
+- (Match_t * A, int N, char * label)
++ (Match_t * A, int N, const char * label)
+
+ // Process matches A [1 .. N] and output them after
+ // a line containing label .
+--- a/src/tigr/show-coords.cc ++++ b/src/tigr/show-coords.cc +@@ -788,7 +788,7 @@ + (vector<AlignStats> Stats) + { + time_t currtime; +- char * type; ++ const char * type; + char date[MAX_LINE]; + long int len; + vector<AlignStats>::iterator Sip; diff --git a/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch new file mode 100644 index 000000000000..97f1dd843aca --- /dev/null +++ b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch @@ -0,0 +1,75 @@ +Use portable shebangs instead of hardcoding interpreters +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/scripts/dnadiff.pl ++++ b/scripts/dnadiff.pl +@@ -1,4 +1,4 @@ +-#!__PERL_PATH -w ++#!/usr/bin/env perl + + #------------------------------------------------------------------------------- + # Programmer: Adam M Phillippy, University of Maryland +--- a/scripts/exact-tandems.csh ++++ b/scripts/exact-tandems.csh +@@ -1,4 +1,4 @@ +-#!__CSH_PATH -f ++#!/usr/bin/env csh + # + # Find exact tandem repeats in specified file involving an + # exact duplicate of at least the specified length +--- a/scripts/mapview.pl ++++ b/scripts/mapview.pl +@@ -1,4 +1,4 @@ +-#!__PERL_PATH ++#!/usr/bin/env perl + + use lib "__SCRIPT_DIR"; + use Foundation; +--- a/scripts/mummerplot.pl ++++ b/scripts/mummerplot.pl +@@ -1,4 +1,4 @@ +-#!__PERL_PATH ++#!/usr/bin/env perl + + ################################################################################ + # Programmer: Adam M Phillippy, The Institute for Genomic Research +--- a/scripts/nucmer2xfig.pl ++++ b/scripts/nucmer2xfig.pl +@@ -1,4 +1,4 @@ +-#!__PERL_PATH ++#!/usr/bin/env perl + # (c) Steven Salzberg 2001 + # Make an xfig plot for a comparison of a reference chromosome (or single + # molecule) versus a multifasta file of contigs from another genome. +--- a/scripts/nucmer.pl ++++ b/scripts/nucmer.pl +@@ -1,4 +1,4 @@ +-#!__PERL_PATH ++#!/usr/bin/env perl + + #------------------------------------------------------------------------------- + # Programmer: Adam M Phillippy, The Institute for Genomic Research +--- a/scripts/promer.pl ++++ b/scripts/promer.pl +@@ -1,4 +1,4 @@ +-#!__PERL_PATH ++#!/usr/bin/env perl + + #------------------------------------------------------------------------------- + # Programmer: Adam M Phillippy, The Institute for Genomic Research +--- a/scripts/run-mummer1.csh ++++ b/scripts/run-mummer1.csh +@@ -1,4 +1,4 @@ +-#!__CSH_PATH -f ++#!/usr/bin/env csh + # + # **SEVERELY** antiquated script for running the mummer 1 suite + # -r option reverse complements the query sequence, coordinates of the reverse +--- a/scripts/run-mummer3.csh ++++ b/scripts/run-mummer3.csh +@@ -1,4 +1,4 @@ +-#!__CSH_PATH -f ++#!/usr/bin/env csh + # + # for running the basic mummer 3 suite, should use nucmer instead when possible + # to avoid the confusing reverse coordinate system of the raw programs. diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml new file mode 100644 index 000000000000..4a3fe8e7bd15 --- /dev/null +++ b/sci-biology/mummer/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">mummer</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mummer/mummer-3.23.ebuild b/sci-biology/mummer/mummer-3.23.ebuild new file mode 100644 index 000000000000..4839053f4191 --- /dev/null +++ b/sci-biology/mummer/mummer-3.23.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="A rapid whole genome aligner" +HOMEPAGE="http://mummer.sourceforge.net/" +SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc" + +DEPEND="" +RDEPEND=" + app-shells/tcsh + dev-lang/perl" + +S=${WORKDIR}/MUMmer${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-3.23-fix-build-system.patch + "${FILESDIR}"/${PN}-3.23-fix-c++-qa.patch + "${FILESDIR}"/${PN}-3.23-fix-shebangs.patch +) + +src_configure() { + use amd64 && append-cppflags -DSIXTYFOURBITS + tc-export AR CC CXX +} + +src_install() { + dobin src/kurtz/mm3src/mummer + dobin src/tigr/{combineMUMs,delta-filter,gaps,mgaps,postnuc,postpro,prenuc,prepro,repeat-match,show-aligns,show-coords,show-tiling,show-snps,show-diff} + dobin scripts/{exact-tandems,mapview,mummerplot,dnadiff,nucmer,promer,run-mummer1,run-mummer3,nucmer2xfig} + newbin src/tigr/annotate mummer-annotate + + insinto /usr/share/${PN}/lib + doins scripts/Foundation.pm + + einstalldocs + use doc && dodoc -r docs/. +} diff --git a/sci-biology/muscle/Manifest 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$CPPNames + do +- echo $CPPName >> /dev/tty +- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt ++ echo "${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o" ++ ${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o + done + + LINK_OPTS= + if [ `uname -s` == Linux ] ; then + LINK_OPTS=-static + fi +-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt +-tail muscle.make.stderr.txt + +-strip muscle +-ls -lh muscle +-sum muscle ++echo "${CXX} ${LDFLAGS} -o muscle $ObjNames" ++${CXX} ${LDFLAGS} -o muscle $ObjNames diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/muscle/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild new file mode 100644 index 000000000000..1e62a9d28eee --- /dev/null +++ b/sci-biology/muscle/muscle-3.8.31.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_P="${PN}${PV}_src" + +DESCRIPTION="Multiple sequence comparison by log-expectation" +HOMEPAGE="http://www.drive5.com/muscle/" +SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="" + +RDEPEND="!sci-libs/libmuscle" +DEPEND="" + +S="${WORKDIR}"/${PN}${PV}/src + +src_prepare() { + epatch "${FILESDIR}"/${PV}-make.patch + tc-export CXX +} + +src_install() { + dobin "${PN}" + dodoc *.txt +} diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest new file mode 100644 index 000000000000..09a566b3b44c --- /dev/null +++ b/sci-biology/ncbi-tools/Manifest @@ -0,0 +1,12 @@ +AUX 21ncbi-r1 232 SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 SHA512 cddde027eb42ce34862c35ad0d809de3738301ea57aec2f84a447efa00eeedbeb528df29390041a1f947dd955d43cabac525316d343aafef001f1de21f5da2d9 WHIRLPOOL d70b9bc3a2b1cdec9c6d2def8b06c70dc0f847992a0720f036a7d2d1e0c90bd8a6a390c7f87c24edd2b0f6326a1d9e0fd0059db20ede0e791cc6ff0c46b8cc70 +AUX ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch 2283 SHA256 fe41b8c4cf389f66471eb5711542b22f3bac2793038fb1d5b427052f30a27de8 SHA512 87cc2442e65d6d3a0fedd2501324834461cfcbbfa9adf83b0f070d5f4d77a1a30c8b9fd22a35263b705c2baefd0dfc11f53d27683b0357d2cd6f74cf379b7979 WHIRLPOOL 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SHA512 be30301617ebbcfe2654ce1994bf7d3c669e61c44a3b093a396269eed426bf4cffc6531ffa86121e15e59814905b3167827fe5d6510c83ec8c078ba1505d21fe WHIRLPOOL 6eb16aef0f2a9bef6158cc421b3b06f48a6876eb522461c3a7620c7a568cdbf9c1d38571b32874f845a584e51a41f981f8bea48916171320cf8606fe16db286c +MISC ChangeLog-2015 19371 SHA256 fe1ad6dc60461f18d0872d550cb87639fa2aa11ef45db9d9576190f2da9461e4 SHA512 a96ef681f1a530cd78c965d91b0779b66e99a1e31e3bab61416a34ec5acef2c0c18cb3caea0aaf16e644999339605fd14106b2d980d7eef5aecef046bc527ff6 WHIRLPOOL dcc15f67e468bb8d5e19fece87472613a5a1b96f7d9272cb11fca8eb1484564cac2eb12c44457e9e357e12628b81ec60427e80b0d906c8b629e0d2502365ecd3 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1 new file mode 100644 index 000000000000..d4de68e6081a --- /dev/null +++ b/sci-biology/ncbi-tools/files/21ncbi-r1 @@ -0,0 +1,6 @@ +# Location of the formatdb data sets +BLASTDB="/usr/share/ncbi/formatdb" +# Location of the BLAST matrixes. +BLASTMAT="/usr/share/ncbi/data" +# Location of the ".ncbi.rc" file which sets the default path for shared data. +NCBI=/etc/ncbi diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch new file mode 100644 index 000000000000..bbc4623609c8 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch @@ -0,0 +1,81 @@ + corelib/ncbilcl.beos | 2 +- + corelib/ncbilcl.hlx | 2 +- + corelib/ncbilcl.lnx | 4 ++-- + corelib/ncbilcl.plx | 2 +- + corelib/ncbilcl.qnx | 2 +- + 5 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos +index f720567..fe6346f 100644 +--- a/corelib/ncbilcl.beos ++++ b/corelib/ncbilcl.beos +@@ -77,7 +77,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx +index 1492f93..0e98fb6 100644 +--- a/corelib/ncbilcl.hlx ++++ b/corelib/ncbilcl.hlx +@@ -67,7 +67,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-/*#define _SVID_SOURCE 1 */ ++/*#define _DEFAULT_SOURCE 1 */ + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx +index 46e2978..b3256b3 100644 +--- a/corelib/ncbilcl.lnx ++++ b/corelib/ncbilcl.lnx +@@ -65,7 +65,7 @@ + * fixes for new RedHat6.2 + * + * Revision 6.3 2000/02/10 16:36:32 vakatov +-* Added _SVID_SOURCE ++* Added _DEFAULT_SOURCE + * + * Revision 6.2 1999/07/12 05:50:49 vakatov + * Avoid redefinition of #_REENTRANT +@@ -141,7 +141,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + #define _GNU_SOURCE 1 + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx +index bf5824c..f2b53e1 100644 +--- a/corelib/ncbilcl.plx ++++ b/corelib/ncbilcl.plx +@@ -68,7 +68,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-/*#define _SVID_SOURCE 1 */ ++/*#define _DEFAULT_SOURCE 1 */ + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx +index c3d1f0a..4b27bd1 100644 +--- a/corelib/ncbilcl.qnx ++++ b/corelib/ncbilcl.qnx +@@ -72,7 +72,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + + + diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch new file mode 100644 index 000000000000..e6763214a6e5 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch @@ -0,0 +1,103 @@ + cdromlib/cdnewlib.c | 6 +++--- + corelib/ncbierr.c | 2 +- + corelib/ncbisgml.c | 8 ++++---- + demo/errhdr.c | 2 +- + 4 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c +index 461292c..be4a2d6 100644 +--- a/cdromlib/cdnewlib.c ++++ b/cdromlib/cdnewlib.c +@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi + char volname[16]; + volname[0] = '\0'; + if (cddev->volume != NULL) +- strncat(volname,cddev->volume->volume_name,sizeof volname); ++ strncat(volname,cddev->volume->volume_name,sizeof volname - 1); + else + sprintf(volname,"entrez%d",cddev->hint); + if (!FileBuildPath(fpath,volname,NULL)) +@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev) + memset((void*)&info,0,sizeof info); + fpath[0] = '\0'; + if (cddev->inf.root !=NULL) +- strncat(fpath,cddev->inf.root,sizeof fpath); ++ strncat(fpath,cddev->inf.root,sizeof fpath - 1); + + if (cddev->ins_volname) + { +@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev) + { + fpath[0] = '\0'; + if (cddev->inf.root !=NULL) +- strncat(fpath,cddev->inf.root,sizeof fpath); ++ strncat(fpath,cddev->inf.root,sizeof fpath - 1); + sprintf(volname,"entrez%d",j+1); + FileBuildPath(fpath,volname,NULL); + if (CdTestPath(fpath,&info)) +diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c +index 0429d86..7b96a2e 100644 +--- a/corelib/ncbierr.c ++++ b/corelib/ncbierr.c +@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx) + if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL) + { + strcpy(path,info->msgpath); +- strncat(path,file,sizeof(path)); ++ strncat(path,file,sizeof(path) - 1); + fd = FileOpen(path,s_msg_mode); + } + +diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c +index 99412be..a653aef 100644 +--- a/corelib/ncbisgml.c ++++ b/corelib/ncbisgml.c +@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t + } + if (i >= num_sgml_entity) + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); +@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t + from++; + if (*from == '\0') + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad); +@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) + } + if (i >= num_sgml_entity) + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); +@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) + from++; + if (*from == '\0') + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad); +diff --git a/demo/errhdr.c b/demo/errhdr.c +index 01cd955..5081489 100644 +--- a/demo/errhdr.c ++++ b/demo/errhdr.c +@@ -41,7 +41,7 @@ int main (int argc, char **argv) + else if (mod[0] == '\0') + { + char *p; +- strncat(mod,argv[i],sizeof mod); ++ strncat(mod,argv[i],sizeof mod - 1); + if ((p = strstr(argv[i],".msg")) != NULL) + *p = '\0'; + } diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch new file mode 100644 index 000000000000..c12feff51af1 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch @@ -0,0 +1,124 @@ + api/alignmgr2.c | 2 +- + api/pgppop.c | 2 +- + api/txalign.c | 10 +++++----- + desktop/seqpanel.c | 4 ++-- + tools/spidey.c | 4 ++-- + 5 files changed, 11 insertions(+), 11 deletions(-) + +diff --git a/api/alignmgr2.c b/api/alignmgr2.c +index 5b43ef3..4b9007e 100644 +--- a/api/alignmgr2.c ++++ b/api/alignmgr2.c +@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn + spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode); + ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1); + buf[ctr] = '\0'; +- fprintf(ofp, buf); ++ fprintf(ofp, "%s", buf); + SeqPortFree(spp); + } + } +diff --git a/api/pgppop.c b/api/pgppop.c +index d16d79d..b359378 100644 +--- a/api/pgppop.c ++++ b/api/pgppop.c +@@ -2994,7 +2994,7 @@ Char DefLine[255]; + if (szSeq){ + if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL, + NULL,NULL)) continue; +- fprintf(fp,szSeq); ++ fprintf(fp, "%s", szSeq); + fprintf(fp,"\n"); + MemFree(szSeq); + } +diff --git a/api/txalign.c b/api/txalign.c +index 5877f9c..cb35fbc 100644 +--- a/api/txalign.c ++++ b/api/txalign.c +@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ + Char checkboxBuf[200]; + sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb); +- sprintf(docbuf+pos,checkboxBuf); ++ sprintf(docbuf+pos,"%s", checkboxBuf); + + pos += StringLen(checkboxBuf); + } + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, +@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + sprintf(HTML_buffer, "<a name = THC%ld></a><a href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\">", (long) oip->id, (long) oip->id); + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, + tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); +@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id); + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, + tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); +@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ + Char checkboxBuf[200]; + sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb); +- sprintf(docbuf+pos,checkboxBuf); ++ sprintf(docbuf+pos,"%s",checkboxBuf); + + pos += StringLen(checkboxBuf); + } +diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c +index 2e78e13..c7538aa 100644 +--- a/desktop/seqpanel.c ++++ b/desktop/seqpanel.c +@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx + seqbuf, alnbuf, &alnbuf_len, + show_substitutions); + MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len); +- fprintf (fp, printed_line); ++ fprintf (fp, "%s", printed_line); + } + fprintf (fp, "\n"); + start = stop + 1; +@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile + seqbuf, alnbuf, &alnbuf_len, + show_substitutions); + MemCpy (printed_line, alnbuf, alnbuf_len); +- fprintf (fp, printed_line); ++ fprintf (fp, "%s", printed_line); + start = stop + 1; + stop += seq_chars_per_row; + } +diff --git a/tools/spidey.c b/tools/spidey.c +index d6ce62d..ac9f59a 100644 +--- a/tools/spidey.c ++++ b/tools/spidey.c +@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose + fprintf(ofp2, " "); + ctr++; + } +- fprintf(ofp2, buf); ++ fprintf(ofp2, "%s", buf); + if (spp){ + SeqPortFree(spp); + } +@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S + ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10); + if (ctr > 0) + buf[ctr] = '\0'; +- fprintf(ofp2, buf); ++ fprintf(ofp2, "%s", buf); + SeqPortFree(spp); + } + done = TRUE; diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch new file mode 100644 index 000000000000..cb7d1adf9208 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch @@ -0,0 +1,37 @@ +--- ncbi-20061015/make/makedis.csh 2006-09-14 17:37:03.000000000 +0200 ++++ ncbi/make/makedis.csh 2007-03-07 21:00:36.090836460 +0100 +@@ -485,6 +485,34 @@ + + set net_stat = $status + ++if ( $net_stat == 0 ) then ++ # Compile additional tools, usually hidden ++ if ( ! $?EXTRA_VIB ) then ++ set EXTRA_VIB = ( asn2all ) ++ endif ++ ++ if ("$?NCBI_MT_OTHERLIBS" == "1") then ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ THREAD_OBJ=$NCBI_THREAD_OBJ \ ++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' ++ else ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' ++ endif ++ eval echo $CMD ++ eval echo $CMD | sh ++ ++ set net_stat = $status ++ ++endif ++ + if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then + echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat + cat <<EOF diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch new file mode 100644 index 000000000000..867b203aecb1 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch @@ -0,0 +1,15 @@ +--- platform/linux-power.ncbi.mk.bak 2005-08-04 22:45:13.000000000 -0500 ++++ platform/linux-power.ncbi.mk 2005-08-04 22:45:35.000000000 -0500 +@@ -9,10 +9,10 @@ + #it appears the flags above do not work anymore with newer libc, + #the new flags should work. Dima. 08/23/01 + NCBI_AR=ar +-NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE ++NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE + NCBI_CFLAGS1 = -c + NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES +-NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE ++NCBI_OPTFLAG = -O3 -D_LARGE_FILE + NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin + NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin + NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc new file mode 100644 index 000000000000..dd77b452fe74 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbirc @@ -0,0 +1,2 @@ +[NCBI] +Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/ncbi-tools/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild new file mode 100644 index 000000000000..cc0e8e3b5472 --- /dev/null +++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild @@ -0,0 +1,164 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic prefix toolchain-funcs + +DESCRIPTION="Development toolkit and applications for computational biology, including BLAST" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/" +SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc static-libs X" + +RDEPEND=" + app-shells/tcsh + dev-lang/perl + media-libs/libpng:0= + X? ( + media-libs/fontconfig + x11-libs/motif:0= + x11-libs/libICE + x11-libs/libX11 + x11-libs/libXft + x11-libs/libXmu + x11-libs/libXt + )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/ncbi" + +EXTRA_VIB="asn2all asn2asn" + +pkg_setup() { + echo + ewarn 'Please note that the NCBI toolkit (and especially the X' + ewarn 'applications) are known to have compilation and run-time' + ewarn 'problems when compiled with agressive compilation flags. The' + ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' + ewarn 'X support is enabled.' + echo +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-extra_vib.patch \ + "${FILESDIR}"/${P}-bfr-overflow.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch + + if use ppc || use ppc64; then + epatch "${FILESDIR}"/${PN}-lop.patch + fi + + if ! use X; then + sed \ + -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ + -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ + -i "${S}"/make/makedis.csh || die + else + # X applications segfault on startup on x86 with -O3. + use x86 || replace-flags '-O3' '-O2' + fi + + # Apply user C flags... + cd "${S}"/platform + sed \ + -e "s:-O[s0-9]\?::g" \ + -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ + -e 's:-x[A-Z]*::g' \ + -e 's:-pipe::g' \ + -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ + -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ + -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ + -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ + -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ + -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ + -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -i * || die + + # We use dynamic libraries + sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die + + sed \ + -re "s:/usr(/bin/.*sh):\1:g" \ + -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ + -i $(find "${S}" -type f) || die +} + +src_compile() { + export EXTRA_VIB + cd "${WORKDIR}" + csh ncbi/make/makedis.csh || die + mkdir "${S}"/cgi "${S}"/real || die + mv "${S}"/bin/*.cgi "${S}"/cgi || die + mv "${S}"/bin/*.REAL "${S}"/real || die + cd "${S}"/demo + emake \ + -f ../make/makenet.unx \ + CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ + LDFLAGS="${LDFLAGS}" \ + spidey + cp spidey ../bin/ || die +} + +src_install() { + #sci-geosciences/cdat-lite + mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die + + dobin "${S}"/bin/* + + for i in ${EXTRA_VIB}; do + dobin "${S}"/build/${i} || die "Failed to install binaries." + done + use static-libs && dolib.a "${S}"/lib/*.a + mkdir -p "${ED}"/usr/include/ncbi + cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ + die "Failed to install headers." + + # TODO: wwwblast with webapps + #insinto /usr/share/ncbi/lib/cgi + #doins ${S}/cgi/* + #insinto /usr/share/ncbi/lib/real + #doins ${S}/real/* + + # Basic documentation + dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} + newdoc "${S}"/doc/fa2htgs/README README.fa2htgs + newdoc "${S}"/config/README README.config + newdoc "${S}"/network/encrypt/README README.encrypt + newdoc "${S}"/network/nsclilib/readme README.nsclilib + newdoc "${S}"/sequin/README README.sequin + mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die + doman "${S}"/doc/man/* + + # Hypertext user documentation + dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} + insinto /usr/share/doc/${PF}/html + doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install + + # Developer documentation + if use doc; then + # Demo programs + mkdir "${ED}"/usr/share/ncbi + mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die + fi + + # Shared data (similarity matrices and such) and database directory. + insinto /usr/share/ncbi + doins -r "${S}"/data + dodir /usr/share/ncbi/formatdb + + # Default config file to set the path for shared data. + insinto /etc/ncbi + newins "${FILESDIR}"/ncbirc .ncbirc + eprefixify "${ED}"/etc/ncbi/.ncbirc + + # Env file to set the location of the config file and BLAST databases. + newenvd "${FILESDIR}"/21ncbi-r1 21ncbi +} diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest new file mode 100644 index 000000000000..9a4df45a3b5e --- /dev/null +++ b/sci-biology/newick-utils/Manifest @@ -0,0 +1,5 @@ +DIST newick-utils-1.6.tar.gz 7518535 SHA256 2c142a2806f6e1598585c8be5afba6d448c572ad21c142e70d6fd61877fee798 SHA512 1e327f9a32b5b0df097bcb63f933f9073a85f0499a2a48be122f4affca52ae1541e1a6e0cca7420447aa8fe8d10d6e76e8d89933b2f84e023d6c87b50808d96c WHIRLPOOL 3d7477a9ffcd2b410d9acf476e2850944dbe361f5c26d7dc853a20d4ec76d70032ab03b5929afa252bda7c24e790243174be8ec35115ba8e78f63eaa332d82d1 +EBUILD newick-utils-1.6.ebuild 399 SHA256 18b1bd684ef09ac049e59ed592a7f88f719d2901bbc68497b728d87166b57e4d SHA512 f359ffd190bf1631108c84ea5230e629b7aa3aa8426d9f3e49b5df4c7d22a75e29bb74215144ab7dfa506dbbec704164c80c58b57c87305314e320c62d764c8d WHIRLPOOL c402cfb1d2ba10412d217bb49da868254a9f8c8055a888024a2bacc7f496ec8be62fa61c11cde4de695891b2471a73bb6cfcdf467418c1a1dc87e86d5e2f12de +MISC ChangeLog 2733 SHA256 cda2035859040337bb964d75ac38a1640791c117c6383061ecf06cde4d0f534b SHA512 175117e51b4fe16f3be312a296339817b6effd8a92cbb2722a9820c71bf7f4f3cf4de3996d79f56ec443321cf40ba4d837640227d55327e7ec962ea9437569db WHIRLPOOL 1ca0cb540f46b9d012522705d8f3b5f9a9026f6c8842eb73ee2f7f538f4c723d8723f57d37b9da874baaaca9d75a7881681eb1ade570bd1447e369f88b77b08c +MISC ChangeLog-2015 987 SHA256 3d747c7f4020369adc9ebc7cc195888ea2ef3b18d7867451363f2d6aff87d177 SHA512 eca65a57252c4f82822bbbc3ebd48a8788d02f6804ddbc92c4652bbde733ffdac8c139798d11be6ae704badf73b3fe1d4c1f720bd263a569d1cef1aee5998cf5 WHIRLPOOL 89be1a116346f1490cde2d8e1b0a1e7ccbab472306d496a1915ad5e1893810cdef3845e453637b3fa8988a6bb18f009cf0b0a7c54ec4bed2af89303811fb1598 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/newick-utils/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/newick-utils/newick-utils-1.6.ebuild b/sci-biology/newick-utils/newick-utils-1.6.ebuild new file mode 100644 index 000000000000..845bc0116205 --- /dev/null +++ b/sci-biology/newick-utils/newick-utils-1.6.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Tools for processing phylogenetic trees" +HOMEPAGE="http://cegg.unige.ch/newick_utils" +SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="!dev-games/libnw" + +src_test() { + emake -C tests check-TESTS +} diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest new file mode 100644 index 000000000000..b90b24102bec --- /dev/null +++ b/sci-biology/njplot/Manifest @@ -0,0 +1,7 @@ +AUX njplot-2.3-buildsystem.patch 1688 SHA256 2ebdf312755f1bb6915ff93959329fa20f92e2b00d681b104858d98e397f2cfb SHA512 af7f9c4e7e20f80e66e78eefb93dce0f99594987fc9ce04de0f447c03e2523b152bd5d32459ab075ca7a65da5d2fb4bb7624e7048f1d6a9ac7c3e1d4b28927b3 WHIRLPOOL 740210f26125ba444544a4394841e16e8e5c584b19ae047faedf7afcc24033caf44b615c7b21c77623efe380a6d34c42a9c46f46b25082a18acb425748478450 +AUX njplot-2.3-format-security.patch 366 SHA256 99bbf3411f8584b3cfbfbeac2c81c3b46ebda7de96279d7a1a0fc625bdec5732 SHA512 1a6a3d823eebca79da482c534f4c7e54e025900dd6f8407a9ae50e997c3585301762da1b0bdd2311f6b5698ba33d96a8fca6b8fada541323a97773146ef8e773 WHIRLPOOL a9736eb7047530d28073791924d79ef9ed65df051cc65b7e432fa9a8abd703131e2f5343266738b7727d43ffca1a918fd2341256aca5472e21a8e0a0e28be856 +DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca +EBUILD njplot-2.3-r2.ebuild 847 SHA256 737901f1562015722d18b658ca43e5de166098a0c393516e38159433c5e9e41e SHA512 8a67dfe8db133776ea7bec00d376c0b25e4044916b1d67659b1a3a8a80c68ef7a90d91005e009acb48fa3f486c7611352639f00067d514cca93a32227a243eb4 WHIRLPOOL 5880a2828b98c1585907354a3fcd50f8298cca8bd557d5ff513cd3398271567c4b20227bad12fbf74498440ae30adaf8fd06bf630cb34fdf74618f73881c433d +MISC ChangeLog 2557 SHA256 e9561fdc8d0a5aec7df0672ed1faca36e91d11656ab7a7de8cfbc09600b42679 SHA512 e0ec62d00ab79b62802ca874215a4f78889b7f5706e135b7a27b04b034547fd001f88efbe3b986604de60848c500afa9723ebf6560b0755ee4ef48b350fe7bcc WHIRLPOOL 8f2297579749ee5079b0d6d7ddefc4af9ebdd871a564ec348fd536acd7cd11ff1cb6e0fbdd84dccde0da93e000ab61c9cc01dfd91ef9cfb7efff3d2600f2eb20 +MISC ChangeLog-2015 2256 SHA256 4958d1e7fa4caf5f2ad1ba69e7f8daf40ed151d58c0a6808956f09cb8a23c0bb SHA512 06c63bb851ce2f5bd3e6fd5aa58d0a46da8940eb81e99fd061cc9f8e3ee8093933d67b8f8c89264a54fa83d3531dcf2e18265b3894c09414f3eac8bb45884d23 WHIRLPOOL 2fd74b27c91b66c91cfa9455365a259e797470b747800d523c87de9192ab0c93794c5742e595d9258ca97f0d0f946f78ed0c67da63e641c54d2ddb3ae873500e +MISC metadata.xml 623 SHA256 a62d170844dfa49cc9e1b16e6316f6681be21207953d7b4a3332e35b6c69a4fe SHA512 494c11097c9484cfb104a8da218202294d13e71b2a8216342c7b9b7f00a97ac19403a3f21db91de08bc38e1bbed39693bd13167b70daad40267dca5fa30e2ff1 WHIRLPOOL 7e0336a4e039f1d4d373ea044e4c46b7d893939f063c12626500d986bfe2d2e975e5e8214b8558cf87bfec1036bfcaf4cec318bbc8b2a5003b081917e94c6874 diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch new file mode 100644 index 000000000000..61f8b95ea160 --- /dev/null +++ b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch @@ -0,0 +1,59 @@ + makefile | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/makefile b/makefile +index ccb7dc2..9488c2a 100644 +--- a/makefile ++++ b/makefile +@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF + #PDFLIB = -L$(PDF) -lpdf + + # c compiler and linker +-CC = gcc ++CC ?= gcc + + # Vibrant top directory +-VIBRANT = /banques0/ncbiJun04 ++VIBRANT = /usr/include/ncbi + + + # X11 include directory +@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o + OBJUNROOTED = unrooted-vib.o preptree.o + + +-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ ++CFLAGS += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ + -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ +- -Wimplicit-function-declaration -g ++ -Wimplicit-function-declaration + + all: njplot unrooted newicktops newicktotxt + + + njplot : $(OBJECTS) +- $(CC) -g -o njplot $(OBJECTS) \ ++ $(CC) $(LDFLAGS) -o njplot $(OBJECTS) \ + -L$(VIBRANT)/lib \ + -lvibrant -lncbi \ + $(PDFLIB) \ +@@ -40,16 +40,16 @@ njplot : $(OBJECTS) + -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm + + unrooted : $(OBJUNROOTED) +- $(CC) -g -o unrooted $(OBJUNROOTED) \ ++ $(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \ + -L$(VIBRANT)/lib -lvibrant -lncbi \ + -L$(MOTIFLIB) -lXm \ + -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm + + newicktops: njplot-vib.c +- $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm + + newicktotxt: njplot-vib.c +- $(CC) -DTTY -o $@ njplot-vib.c -lm ++ $(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm + + + .c.o : diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch new file mode 100644 index 000000000000..686b8475e9ed --- /dev/null +++ b/sci-biology/njplot/files/njplot-2.3-format-security.patch @@ -0,0 +1,16 @@ + njplot-vib.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/njplot-vib.c b/njplot-vib.c +index fe55609..63fd3b6 100644 +--- a/njplot-vib.c ++++ b/njplot-vib.c +@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" + #else + fprintf(stderr, + #endif +- message); ++ "%s", message); + exit(0); + } + } diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml new file mode 100644 index 000000000000..4cdb5abfd7a5 --- /dev/null +++ b/sci-biology/njplot/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + NJplot is a tree drawing program able to draw any phylogenetic tree + expressed in the Newick phylogenetic tree format (e.g., the format used + by the PHYLIP package). NJplot is especially convenient for rooting the + unrooted trees obtained from parsimony, distance or maximum likelihood + tree-building methods. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild new file mode 100644 index 000000000000..420861dac42b --- /dev/null +++ b/sci-biology/njplot/njplot-2.3-r2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-biology/ncbi-tools[X,static-libs] + x11-libs/libXmu" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-format-security.patch + "${FILESDIR}"/${P}-buildsystem.patch +) + +src_prepare() { + default + sed -i -e "s:njplot.help:${EPREFIX}/usr/share/doc/${PF}/njplot.help:" njplot-vib.c || die + + tc-export CC +} + +src_install() { + dobin newicktops newicktotxt njplot unrooted + doman *.1 + dodoc README njplot.help +} diff --git a/sci-biology/pals/Manifest b/sci-biology/pals/Manifest new file mode 100644 index 000000000000..d99fecd865d5 --- /dev/null +++ b/sci-biology/pals/Manifest @@ -0,0 +1,6 @@ +AUX pals-1.0-fix-build-system.patch 681 SHA256 5c76d6c96a86b41dd2233664e2c46b4f1b2dbd3eb568bc6f1f43d1d9f6341e0f SHA512 bd95517d72cf567a4608878d556919396c9dd1cd77a4e49f2f8604f058c76a1f26c31760ad6ef6048ec12b76de46a6f4c56b5cb27b4aa1f91339c8f14bd963ac WHIRLPOOL d4c573a048bff7128f83a8a9816bc357cd18822cd4207877bc0a45dcedc834518c6f7cfd7895f1dd5f8f5e909366df197778776721e2e09dd0c4cb46ccba2176 +DIST pals-1.0.tar.gz 24895 SHA256 2768adfdd93f56f859744ff9bbbabcc4571b38fa8ea247d505599beee3a962c2 SHA512 655e3311c63709dab1f8a13b193ed30a5ee97c04757a1e8408a74f6110ff3bdd96ba9eb07f4987ed5b83790ffa8cec67f722fee783c4ab4120483a683ebb9b8f WHIRLPOOL 2cfc45858796a5a0a01287cd3b5a7235e90371e092dfe1a90b9c394e8334e16fb01766c6824ca606a86de48740a8036c695517d6797fd6682a7c8fd6bd6ebb02 +EBUILD pals-1.0-r1.ebuild 537 SHA256 cac9bef59956ece082e1736ad589ced57c78ae683b7a8341c6ee2da813bd95ec SHA512 666542e4faefb47a94ab6f7cc3be531f39e2ca3f68324a80bafbccc6c0de162d2a20dbda507709cfd2f207b61734aa21211a93bd597b02599d9648ca557d4b4e WHIRLPOOL 628aa8e53256b17a7e3c8572800198cc59ae6c88edb4dda4f4e103e8c8014ba568024826e9a3ee98e45b2febe4ee8cafd11c5888fb26fe434de70cd5a26f7d28 +MISC ChangeLog 2417 SHA256 74412c43e82063d034da51de2dc2ee4715aaafcee6f221e87adeb5d757f47739 SHA512 091097d1e4fce97c70ac60981a49cda99d6aa0c810f3deeace079a53863ee26444abf1ff665b3da0490bce22bf0fbaaf6f870b4720e29a9dd71c66e80949e666 WHIRLPOOL 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file mode 100644 index 000000000000..a020a697f85b --- /dev/null +++ b/sci-biology/pals/files/pals-1.0-fix-build-system.patch @@ -0,0 +1,34 @@ +Make build system honour user variables + +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,4 @@ +-CFLAGS = -O3 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -Winline -DNDEBUG=1 +-LDLIBS = -lm -static +-# LDLIBS = -lm ++LDLIBS = -lm + + OBJ = .o + EXE = +@@ -8,18 +6,13 @@ + RM = rm -f + CP = cp + +-GPP = g++ +-LD = $(GPP) $(CFLAGS) +-CPP = $(GPP) -c $(CFLAGS) +-CC = gcc -c $(CFLAGS) +- + all: pals + + CPPSRC = $(sort $(wildcard *.cpp)) + CPPOBJ = $(subst .cpp,.o,$(CPPSRC)) + +-$(CPPOBJ): %.o: %.cpp +- $(CPP) $< -o $@ ++%.o: %.cpp ++ $(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@ + + pals: $(CPPOBJ) +- $(LD) -o pals $(CPPOBJ) $(LDLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o pals $(CPPOBJ) $(LDLIBS) diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/pals/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pals/pals-1.0-r1.ebuild b/sci-biology/pals/pals-1.0-r1.ebuild new file mode 100644 index 000000000000..32579b9d0757 --- /dev/null +++ b/sci-biology/pals/pals-1.0-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Pairwise Aligner for Long Sequences" +HOMEPAGE="http://www.drive5.com/pals/" +SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S=${WORKDIR} + +PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch ) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin pals +} diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest new file mode 100644 index 000000000000..d91078ef56e8 --- /dev/null +++ b/sci-biology/paml/Manifest @@ -0,0 +1,5 @@ +DIST paml4.4c.tar.gz 2891715 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a WHIRLPOOL 44ae42dd6088039be1041cdce70ce9ee907b8f85d4e25f9d556df4738ea3ea91f700f96f627f20a13d226038132fd23aecbc5b452bfb6716b9499c8d2be491e4 +EBUILD paml-4.4c-r1.ebuild 983 SHA256 b26af56a27830d61800dcde4748c7bf8e22e7bdcc5bf64ca699fadc7bc202cfa SHA512 a7d590056e148c08607c6c15e872f6fc4ea87166336f19eeef497efb4852481b782b83f8e40b6f50005dffaa45b1fb6d028cd101fd54efa643e3678e60836b04 WHIRLPOOL 06bcfe96dc03e4e7a53973485fe857326543d3f0cfaddc69b82100d7afacd3cfa0d46cfbbf296fc34c03e160f8d332daed07fae8e9b4333620b4b04aed1f4568 +MISC ChangeLog 2425 SHA256 d403a8cfba0398d18886db184fe791caaeca0a0491f2d071f83786aa12fe8d05 SHA512 8906f03dc75d0a5b1e986df0a1f67d3a7eadcb7faeed673e20744d5df93d01f6703cae009e329cebc11798d3d8a4310174106dcd3928915ebaf36e76444de534 WHIRLPOOL 0f080599fbecf90cd407a61052c36b20679e633f967539fd6acde91b5fb803e5a9773d890bae96c3436d0d8f1ffdaa9c4c055d1606b7412212400a360b9da4c4 +MISC ChangeLog-2015 2630 SHA256 6c2d59aeba797855630a7d38aaae91f36b31d2b2a48e71a7798d89901a3bffe6 SHA512 baed8489c9c2684a208f9f42096a299d268048ea19a0c71e43bc4f17a9f8438f14ab702c31bb4c252bddd6452469fa7641ba6694a7899d22ab9ee2f02df8f8eb WHIRLPOOL 19701038e949a640bedf1caada118ec3272591c45f215c66c0c355fcc5445086f925a7e8e4060064a822ecdec75ad8c4d4765499aaaeda8b25670c9b801febf1 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/paml/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild new file mode 100644 index 000000000000..27fe5ed4c769 --- /dev/null +++ b/sci-biology/paml/paml-4.4c-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs versionator + +MY_P=$(version_format_string '${PN}$1$2') + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" +SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + # Notice send by mail to prof. Ziheng Yang + sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608 +} + +src_compile() { + emake -C src \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dodoc README.txt doc/* + + insinto /usr/share/${PN}/control + doins *.ctl + + insinto /usr/share/${PN}/dat + doins stewart* *.dat dat/* + + insinto /usr/share/${PN} + doins -r examples/ + + cd src || die + dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 +} diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest new file mode 100644 index 000000000000..d09e0882b062 --- /dev/null +++ b/sci-biology/phrap/Manifest @@ -0,0 +1,6 @@ +AUX phrap-1.080812-fix-build-system.patch 3600 SHA256 ce995ffdad2e8d5d63e3a095e9c7616fdc94f6a7d4401c554f3359e673ac7f3c SHA512 536ad862b9b8ce0fbc7ab67bc48db597e7d4b8c66018a5abefe5a59f4fbc30a4a76c94f4c13f5af7d42a422a22f5181d8f015b797d37f175238c3d4170adf21c WHIRLPOOL 4a4dd715bc8c71705789997a3039c07f6148f17463c9afe0456c5a9d09de4483f12923897f89cf230819476344386a40d7e926ddaf4d432ffee2d9212c413c00 +DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca WHIRLPOOL e516561804620ba8c96ed0e5c5d791f3fe1e7984e08f646e6fd7c30042f2550f5d1c9b2f800e8a853e42b049b92418ed9d0121e77bf4e9aa895974bce5e73717 +EBUILD phrap-1.080812-r2.ebuild 950 SHA256 b98d56ca4718e86872195133dc4abcbc8308faad70cb958f87c08d0228907239 SHA512 4857f1fe337f24ee33618e3dac40a5edb7210d1353c058b57a1263a4ccdd8213270827c2c2f902d454226fc65368a1588d497dcdcf2eb9c15af406d1d5cac3fe WHIRLPOOL 45f46d85e8030d8e3b1ab805b97b25b731dde1956ec39c143e7507325294c43ddd780583ab7edd074bfd9161ce6c6a8e46ccc1abb726b69c85922645dd7ff613 +MISC ChangeLog 2829 SHA256 00f1db92cfbee3d80b26fe8193ef549bd70b5900d7819b9b9cdec54f76449170 SHA512 c98163ea771352ee0930a181ebbdb521a5c9057216afee402ea5edfb784c2ec316ce6c79076a8d1be2999d9d6a01355ebf5ce203322946b16035105b9fb05f6d WHIRLPOOL 94cda4fe5d3c0abd581484bf7ef7bf8292d5d727e2eaeb2d40fa8584f54273d5b34f60e7969ab7a6583bb931e18f981445c00a651796b431572e5691e81a1da2 +MISC ChangeLog-2015 948 SHA256 e18d1784109b55db14e7b9a4fb61e5d4b66813e114669c28420953cb014b6be5 SHA512 f23fd3cf92ef5071d962702da3bd3253b949a1982ea4a67d9ea09308c6bec3811753916b37a3853c02b199bcb56245549c8d84dc7bbb84eb2cf3dcd6ad158f6e WHIRLPOOL f44d52aa4612ccf877d37ad97102a4a8d565e406b68805e366e573f179beda0d2076268298d1905202c2958d23f69bcee8e5a018ad6874cb7308a858d9151176 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch new file mode 100644 index 000000000000..6d30c2ce326a --- /dev/null +++ b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch @@ -0,0 +1,100 @@ +* Fix perl shebang to be portable +* Make build system honour LDFLAGS + +--- a/makefile ++++ b/makefile +@@ -25,9 +25,8 @@ + # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated) + #CC= icc + #CFLAGS= -O2 -wd266,880 +-CC= cc +-CFLAGS= -O2 +-LFLAGS= -lm ++CC ?= cc ++LIBS = -lm + + SWATOBJS= swat.o weibull.o + +@@ -96,46 +95,46 @@ + chmod a+x phrapview + + swat: makefile $(SWATOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS) + chmod o-r swat + + alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) + chmod o-r alpha_swat + + swat_counts: makefile $(COUNOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) + chmod o-r swat_counts + + swprobs: makefile $(PROBOBJS) +- $(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS) + + phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r phrap + + gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) +- $(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) + chmod o-r gcphrap + + cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r cross_match + + gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) +- $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS) + chmod o-r gccross_match + + cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS) + chmod o-r cluster + + loco: makefile $(LOCOOBJS) $(SWOBJS) +- $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS) + chmod o-r loco + + erf_test: $(ERFOBJS) +- $(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS) + + loco.o: swat.h + +@@ -228,7 +227,7 @@ + anomalies.o: swat.h + + fast_smith_wat.s: fast_smith_wat.c +- cc -S -machine_code -source_listing -O3 fast_smith_wat.c ++ $(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c + #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!! + + tig_node.o: swat.h +--- a/phrapview ++++ b/phrapview +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl + + + #/***************************************************************************** +@@ -25,6 +25,7 @@ + # + #*****************************************************************************/ + ++use warnings; + use strict; + use Tk; + #phrapview version 0.960731 diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/phrap/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild new file mode 100644 index 000000000000..6cccc6c61bf0 --- /dev/null +++ b/sci-biology/phrap/phrap-1.080812-r2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Shotgun assembly and alignment utilities" +HOMEPAGE="http://www.phrap.org/" +SRC_URI="phrap-${PV}-distrib.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + dev-lang/perl + dev-perl/Tk" + +S="${WORKDIR}" + +RESTRICT="fetch" +PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" ) + +pkg_nofetch() { + einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file" + einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\"" + einfo "and put it in ${DISTDIR}" +} + +src_compile() { + emake CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin cross_match loco phrap phrapview swat + newbin cluster cluster_phrap + + local i + for i in {general,phrap,swat}.doc; do + newdoc ${i} ${i}.txt + done +} diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest new file mode 100644 index 000000000000..d9d00191b287 --- /dev/null +++ b/sci-biology/phred/Manifest @@ -0,0 +1,7 @@ +AUX phred-071220-fix-build-system.patch 1981 SHA256 dcdce5aa8e23689a8d0b59f7ce0d2f336c894588e70b86a40ad2aa7de266cac0 SHA512 7647f6f6e9a1ae51cbf1aa3e39b337288e22fc26a95fdd88f92ce43fc6c0ef6ff59ec26919d14dfefff70be48e4a5604ddefef98bddf5d1d14d1e656665c878d WHIRLPOOL 7b6d72d7263d388e56c9cba872f193e0741fa1d8e55f03f53636ac2867a99b6d315bab84c70b062cca5a5fcb525878f307f336946f9fdc5dbffc9e51a24ce3ac +AUX phred-071220-fix-qa.patch 787 SHA256 696031eca7f55242ca002e37ca8a38f27e0f05c00572fb3cdad1636c72146ea1 SHA512 27811a834358d0e1bf8281882e0420e0eb6bd9586871c8c72a4de79badc9539ea8e9258b9c3a3bf8ca1d3f6924d61abce2dcc0c0ed3b64e5fa53d4548109f5bc WHIRLPOOL cc076f36d40d60fc2eab11d5ac0007661362afdaa35c1b9f5eefcf1e08a0862952d05f1aa5c9a752a747040aeab7057b6c97b34c6d7253c16bb032535bae6477 +DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975 SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 WHIRLPOOL 9b14cfb1ca970a14ef613ca17efb82955c0ecec414dfad8835c883650f306b3a79846b7a410a9359cbd9ca953d890673366b6f865a2a357e81213d34b3327d3e +EBUILD phred-071220-r1.ebuild 966 SHA256 51a4aee5de28daa085f086ef5aed2526aeede8c73be341a1a0f8c5640f0fbc92 SHA512 203ced3280f1c1bced57a1cb514533b71df1c2c9eefc94e594f61d45300da32617ff6023196d47cab7a1ca21bef61392760f5a12f25815ac5d78b9a8c58e7e91 WHIRLPOOL 73f20affc430537562a46d8f32cbe271e6c0c38854b33a1f689a9ba640583e4deee0753ef0986483fbb3a2845f46b020e30fc4fe3e67578d3b4be8c63ffdd30d +MISC ChangeLog 2691 SHA256 35005c4acf5310f01e34dc177f0791ef5053dbd9d8d3ee0bba147c409b1cd4b2 SHA512 d494e7bfeb3cc57ff9129c7c27f3296b156fad75a59d9a12ea7edfb8f26d14228e9e1cb1e7caf19dde1253d1581754e7030f61f79470ab0a9ae7fb9dd40160b6 WHIRLPOOL e5a408d79f41596f57e53baf344512a5b2670da36ac894f8fcc28898aa8806bc1d5a42b83c5956a47645b1c5286d6748d7f0e2bd718f3821ac902bfe36dca4fd +MISC ChangeLog-2015 716 SHA256 04a912e65a0223189d465ec11e8c64f177086b763b51f095826488cbafa5c654 SHA512 31af3a92ad7829c0e92b01c11a04acd3b6b626ea2479baafe807bb3fedc8b2bbfbcd6d16ace795c16df815a2d0ce09431d2b6fd7e7a71032db163ece4e0ae6d6 WHIRLPOOL b02865f737d32a4a74e7e73757bf6dabe464a17b080a18da8786da6bec12fd3b792b2b134da7a15400f4fc25b695b24e1d1ce65b6f0568ae70499ae77eda43b3 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch new file mode 100644 index 000000000000..997f39941a07 --- /dev/null +++ b/sci-biology/phred/files/phred-071220-fix-build-system.patch @@ -0,0 +1,82 @@ +* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS +* Specify a default target, in order to keep the ebuild slim + +--- a/Makefile ++++ b/Makefile +@@ -12,9 +12,9 @@ + + # UNIX specific definitions (default) + # +-CC= cc +-CFLAGS= -O -DANSI_C $(LXFLAGS) +-CLIB= -lm ++CC ?= cc ++CPPFLAGS += -DANSI_C $(LXFLAGS) ++LIBS += -lm + + # Windows 'nmake' specific definitions + # +@@ -133,9 +133,6 @@ + $(objdir)writeSDF.o \ + $(objdir)writeSeq.o + +-SRCS = $(OBJS:.o=.c) +-WOBJ = $(OBJS:.o=.obj) +- + INCS = \ + $(incdir)chromatData.h \ + $(incdir)freeChromatData.h \ +@@ -179,48 +176,18 @@ + # UNIX make specific phred target + # note: a horizontal tab character must precede `$(CC)' + # +-phred: $(OBJS) +- $(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB) + + +-# Windows nmake specific phred target +-# +-forwindows: $(WOBJ) +- $(CC) $(CFLAGS) /Fephred $(WOBJ) +-# $(CC) $(CFLAGS) /Fedaev daev.c ++.PHONY: all ++all: phred daev + + +-# test CC: refuse to compile if +-# +-# o SunOS +-# +-# AND +-# +-# o using /usr/ucb/cc compiler +-# +-# NOTE: this compiler causes problems: see PHRED.DOC +-# +-test_cc: +- @if [ `uname` = SunOS ] ; \ +- then \ +- if [ `which $(CC)` = "/usr/ucb/cc" ] ; \ +- then \ +- echo ""; \ +- echo "============================================================"; \ +- echo "| |"; \ +- echo "| This SUN C compiler produces a bad phred executable. |"; \ +- echo "| |"; \ +- echo "| Please see the PHRED.DOC file for more information. |"; \ +- echo "| |"; \ +- echo "============================================================"; \ +- echo ""; \ +- exit 1; \ +- fi \ +- fi ++phred: $(OBJS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS) + + + daev: daev.o +- $(CC) $(CFLAGS) -o daev daev.o -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS) + + + clean: diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch new file mode 100644 index 000000000000..ab4d2ea023f6 --- /dev/null +++ b/sci-biology/phred/files/phred-071220-fix-qa.patch @@ -0,0 +1,36 @@ +Fix implicit declarations: +* daev.c: In function ‘processParameters’: +* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration] +* if( !isdigit( argv[iarg][0] ) ) + +--- a/autoPhred.c ++++ b/autoPhred.c +@@ -57,6 +57,7 @@ + static int xstrcmp(); + #endif + ++int freeMBRData( MBRData *mbrData ); + #ifdef ANSI_C + int autoPhred( Option *option ) + #else +--- a/daev.c ++++ b/daev.c +@@ -58,6 +58,7 @@ + #include <sys/stat.h> + #include <time.h> + #include <math.h> ++#include <ctype.h> + + #ifndef _WIN32 + #include <dirent.h> +--- a/mergedBaseRead.c ++++ b/mergedBaseRead.c +@@ -63,7 +63,7 @@ + Peak *peak; + Observed_peak *obs_peak; + +- static initFlag = 0; ++ static int initFlag = 0; + static char mchar[256][256]; + + if( initFlag == 0 ) diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/phred/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/phred/phred-071220-r1.ebuild b/sci-biology/phred/phred-071220-r1.ebuild new file mode 100644 index 000000000000..e09c456b27d9 --- /dev/null +++ b/sci-biology/phred/phred-071220-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="A base caller for Sanger DNA sequencing" +HOMEPAGE="http://phrap.org/phredphrapconsed.html" +SRC_URI="phred-dist-071220.b-acd.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}" + +RESTRICT="fetch" +PATCHES=( + "${FILESDIR}/${PN}-071220-fix-build-system.patch" + "${FILESDIR}/${PN}-071220-fix-qa.patch" +) + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "${SRC_URI}, then place it in ${DISTDIR}" +} + +src_compile() { + emake CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin phred daev + + insinto /usr/share/${PN} + doins phredpar.dat + + echo "PHRED_PARAMETER_FILE=${EPREFIX}/usr/share/${PN}/phredpar.dat" > 99phred || die + doenvd 99phred + + newdoc DAEV.DOC DAEV.DOC.txt + newdoc PHRED.DOC PHRED.DOC.txt +} diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest new file mode 100644 index 000000000000..5010dafb9cf6 --- /dev/null +++ b/sci-biology/phylip/Manifest @@ -0,0 +1,8 @@ +AUX README.Gentoo 643 SHA256 d8a737f2ca6e0366fcebb96fbc9e12200b6402fea4c4f71696f4d9175980dfbd SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a WHIRLPOOL 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SHA512 b7d6638ddc1a035132507918dd49e82e41e450ca31b8e6afbf646e69ce29690b5be74795a108a03eaf79399bc909031d844f664e072861f4cc656aaa0b8946c7 WHIRLPOOL f0d6237fe45518ca5ec4400889ad1f381c964e4bf5792224c31a9c103f30102d082805dccd7ac95ee20341da94de48c300ac1133d2ff5dee5e1b47ba4bb0b1b0 +EBUILD phylip-3.696-r1.ebuild 1134 SHA256 48032ba78c33af8b36b53aafbf455e5419a556e0e38782fdee5a77887ac43704 SHA512 ef7196f540a1bf981dd1d2489fc2cba31fd0ea3135f060331f8f1ba43ce585ae4c6d33cc76f53d561c1c36059c631303caeaa20c28ada2c02ce218119a202872 WHIRLPOOL 56fb7f7895b25362b7ef60e17be8cca51c931e06de6f4b6f23073652e6ed71cfd87856d2ae3f6252011fa9c87765454a2495f44df32357cd5f4d875eb7f20f89 +MISC ChangeLog 2875 SHA256 795996871597ce5b9b96ecbd7e72fa271b2dceda9d172b42af4ef1583207dde8 SHA512 c62f9a8b3cc0d1a7b5f532c7fffeafa95019d868e9dbb789c53342e326259402aaa85f14fb3b50816e4453652a79cfd7eaa675895e032204383bc0d83f2300a4 WHIRLPOOL 5809f10fde8471e47635ba845f959bcd5544b30d047499ae8656b0108dd686585102552706372bf5b6b70b4b0e6d14899ee15860492766ea97366514b6d382dc +MISC ChangeLog-2015 7026 SHA256 733a3765122ab15458e701cbf902f9408672e47696b84f971182f968e70129bd SHA512 fa87c1d1959303b6d8e402812c1600cd5868724c93e4e8a6bee14f9ec320f8e967da5f443622c39e476b17b6bbe90006e52a0cfcaab8504a23267af74d79c897 WHIRLPOOL 1fb268aea348f615a17c2bee08c81592ff1ea20934cb5ab0b634adb5f490179efecdd67e446308a84f4e562067971dcc5db5935a755bea995969db65d1e81b50 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/phylip/files/README.Gentoo b/sci-biology/phylip/files/README.Gentoo new file mode 100644 index 000000000000..3b2062003996 --- /dev/null +++ b/sci-biology/phylip/files/README.Gentoo @@ -0,0 +1,15 @@ +Using the PHYlogeny Inference Package on Gentoo systems + +Location of the factor program + +On Gentoo systems, the PHYLIP program "factor" is named "factor-phylip", in +order to avoid a file collision with the program of the same name provided by +the "sys-apps/coreutils" package. + +Location of the font files + +PHYLIP programs will find font files only if they are in a directory +referenced by the "PATH" variable or if they are in the current working +directory. When working with PHYLIP programs that need these files, either +copy or symlink the fonts you need to your working directory, or add +"/usr/share/phylip/fonts/" to your "PATH" variable. diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/phylip/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild new file mode 100644 index 000000000000..658c92e785c2 --- /dev/null +++ b/sci-biology/phylip/phylip-3.69-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION=" The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" +SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" + +SLOT="0" +LICENSE="freedist" +IUSE="" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND="x11-libs/libXaw" +DEPEND="${RDEPEND} + x11-proto/xproto" + +S="${WORKDIR}/${P}/src" + +src_prepare() { + sed \ + -e "s/CFLAGS = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \ + -e "s/CC = cc/CC = $(tc-getCC)/" \ + -e "s/DC = cc/DC = $(tc-getCC)/" \ + -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ + -i Makefile || die "Patching Makefile failed." + mkdir ../fonts || die +} + +src_compile() { + emake -j1 all put +} + +src_install() { + cd "${WORKDIR}/${P}" || die + + mv exe/font* fonts || die "Font move failed." + mv exe/factor exe/factor-${PN} || die "Renaming factor failed." + + dobin exe/* + + dodoc "${FILESDIR}"/README.Gentoo + + dohtml -r phylip.html doc + + insinto /usr/share/${PN}/ + doins -r fonts +} diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild new file mode 100644 index 000000000000..03b33b303805 --- /dev/null +++ b/sci-biology/phylip/phylip-3.696-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION=" The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" +SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD-2" +IUSE="" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND="x11-libs/libXaw" +DEPEND="${RDEPEND} + x11-proto/xproto" + +S="${WORKDIR}/${P}/src" + +src_prepare() { + mv Makefile.unx Makefile || die + sed \ + -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ + -i Makefile || die "Patching Makefile failed." + mkdir ../fonts || die +} + +src_compile() { + emake -j1 \ + CC="$(tc-getCC)" \ + DC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" \ + all put +} + +src_install() { + cd "${WORKDIR}/${P}" || die + + mv exe/font* fonts || die "Font move failed." + mv exe/factor exe/factor-${PN} || die "Renaming factor failed." + + dolib.so exe/*so && rm exe/*so || die + dobin exe/* + + dodoc "${FILESDIR}"/README.Gentoo + + dohtml -r phylip.html doc + + insinto /usr/share/${PN}/ + doins -r fonts +} diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest new file mode 100644 index 000000000000..ee94a3c2ecce --- /dev/null +++ b/sci-biology/phyml/Manifest @@ -0,0 +1,6 @@ +AUX phyml-2.4.5-fix-build-system.patch 1735 SHA256 0635b908cfb0b5cd58dfe7bffd22c6b5f24e8cca4f0ba077062831377649b0b5 SHA512 95079d00d4a7373f9b6f9b17b707ae999db38a341e03f96b5f1b023ea4fd76a4027f6a46c6e33ecf7902ab4dcbc22d199b5c0f75a7b0059c90f7c11fbc9146cf WHIRLPOOL 63bd683e9d57172a53a2bb65ecca0d781b249d73ae8db092c615524666d00b0cc89a9bec80f7678b1d9883c48d3b0a09c131303377da73cf454ae7c74eca6120 +DIST phyml_v2.4.5.tar.gz 92143 SHA256 e8a1d3980137f8e528d0e59472aff37dbac615860a7d3ee4cdb64f30dfea296e SHA512 119716290eca0de4da05b0bacbec96139f4c89f6a033b861d1cb2655a620766bd0bea0675c4d7722a31d888652a28bf3544a643f39f11682982ede80dc5928c3 WHIRLPOOL e9c0e36ea871c61fc617ed0a10d306bdb66d84da0b9a08107fb9e1f6370e10676c5ad8a0a5e5404ccad6ae2f62551d566614a173cfdd4a0a523f727fc7924ce0 +EBUILD phyml-2.4.5-r3.ebuild 538 SHA256 22bf7f9b8b325d70ff7ee5e63207e2cb94a0fd0b0a2f723c623a7aad6753f090 SHA512 72a9907fa91529e696da775b9b99282c3df09e79d01a793601d949a593c05870ee0086c596fded675c1ef485f2d3a8d618447493ce90a786015a85a3848ec7e7 WHIRLPOOL 3ed65d9bce2c3313f1a08111388ac6c44c328cc9e66ca3237ced0ec07752af63584bba7181886b745a1b0c47c785b3bb859efdd457948f462bdad2aeca0b814f +MISC ChangeLog 2430 SHA256 d2024494a36343204465656b7b40db70cfcce68862a2ea52217fb2e0fafbee1a SHA512 1154e0a5002833a4be31df6686f0847daa4495af1175544d61928cbf6ce534ccafebbc33eb8946eb7721d1bd1298bf2458f50ac078d355492101f3fc499ea134 WHIRLPOOL fe22e48888de5c18570f7b1deabddfbd2d9949bab745808e294a2965332fce6b451e5b3229c895e3eb3dfcd5410b0af346da00ee363715b46cff42e54c8a972a +MISC ChangeLog-2015 1617 SHA256 ffa16cf31a589b692e8eeb21f9aebdb4ff68f52c50814178f65c6ebf1f9aab76 SHA512 b30f1127d8e02b6ba3e3860d604fcfc57cad9ef4f633faa20783bab48c54adbd4dbf5c472c43e5204b472574a3966d9aa579e3f0ee1880321ad8ea8c0a610630 WHIRLPOOL 93bfdd0d44b46ae9af184cbdd915c99000691e7395d1a280ec097d333cd11eb0c447b29a693dd42ea32d3c5959310ee8e9306889578f7925c92169ab640f8950 +MISC metadata.xml 574 SHA256 94713e777819ed96a655c5806190e2d62fd824bbd1c9242071505fc31476ba23 SHA512 0f25e0d422671c08446bd97be45b2f00e95cf793666ee6ece0652eeb8e27fd983896e3f865f4e5d7a04231355bbd6047dd19dac0ce3490ec78562305255c1a2b WHIRLPOOL 79885b18e00ff582d6746b0efef1b34901935edd9f4a753751ea846201264652b143418dad2a1a8d950cc52ab456a8fe272616ee2e8aa9c34b142ebc0859d48e diff --git a/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch new file mode 100644 index 000000000000..9b1d9e03ca14 --- /dev/null +++ b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch @@ -0,0 +1,67 @@ +Fix build system to honour user flags. + +--- a/Makefile ++++ b/Makefile +@@ -1,10 +1,4 @@ +-hello !!! +- +-CC = gcc #cc +-CFLAGS = -O4 -fomit-frame-pointer -Wall -static +-# CFLAGS = -Wall +-# CFLAGS = -g -Wall +-# CFLAGS = -pg -Wall -fprofile-arcs -static ++CC ?= gcc + LIBS = -lm + + PROG = PHYML +@@ -23,39 +17,39 @@ + + + $(EXEC) : $(OBJS) +- $(CC) -o $(EXEC) $(OBJS) $(LIBS) $(CFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(EXEC) $(OBJS) $(LIBS) + + clean : + @rm *.o + ###################################################################################################### + + eigen.o : eigen.c eigen.h +- $(CC) $(CFLAGS) $(DFLAG) -c eigen.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c eigen.c + + simu.o : simu.c simu.h +- $(CC) $(CFLAGS) $(DFLAG) -c simu.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c simu.c + + lk.o : lk.c lk.h +- $(CC) $(CFLAGS) $(DFLAG) -c lk.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c lk.c + + utilities.o : utilities.c utilities.h +- $(CC) $(CFLAGS) $(DFLAG) -c utilities.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c utilities.c + + optimiz.o : optimiz.c optimiz.h +- $(CC) $(CFLAGS) $(DFLAG) -c optimiz.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c optimiz.c + + bionj.o : bionj.c bionj.h +- $(CC) $(CFLAGS) $(DFLAG) -c bionj.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c bionj.c + + main.o : main.c +- $(CC) $(CFLAGS) $(DFLAG) -c main.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c main.c + + models.o : models.c models.h +- $(CC) $(CFLAGS) $(DFLAG) -c models.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c models.c + + free.o : free.c free.h +- $(CC) $(CFLAGS) $(DFLAG) -c free.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c free.c + + options.o : options.c options.h +- $(CC) $(CFLAGS) $(DFLAG) -c options.c ++ $(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c options.c + diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml new file mode 100644 index 000000000000..68536249891c --- /dev/null +++ b/sci-biology/phyml/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription lang="en"> + Phyml is a simple, fast, and accurate algorithm to estimate large + phylogenies by maximum likelihood. Given input sequence files, it + estimates phylogenies using maximum likelihood, and is capable of + processing large amounts of phylogenetic data. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/phyml/phyml-2.4.5-r3.ebuild b/sci-biology/phyml/phyml-2.4.5-r3.ebuild new file mode 100644 index 000000000000..098771430632 --- /dev/null +++ b/sci-biology/phyml/phyml-2.4.5-r3.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_P=${PN}_v${PV} + +DESCRIPTION="Estimation of large phylogenies by maximum likelihood" +HOMEPAGE="http://atgc.lirmm.fr/phyml/" +SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch ) + +src_prepare() { + default + tc-export CC +} + +src_install() { + dobin phyml +} diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest new file mode 100644 index 000000000000..1f11f5f1d299 --- /dev/null +++ b/sci-biology/picard/Manifest @@ -0,0 +1,6 @@ +AUX 1.103-gentoo.patch 5667 SHA256 83eea393354c3802cd367f42762bcbb53ac026c2d12188ca946295347950dd23 SHA512 966b0cc9ffc5bbf4b23c003538e01533344df496c38797ab84fcd2b382e91e003cc797a0c6ff5a878406b1fc169c1b044bce447b68770c665cec327762f08f6d WHIRLPOOL 6771393d7a39cdae83866918ce187d556ed697f41d55032eea85295f08cc660542136a9f9eaa23f9cec014743aa0099303c1cee206a0318951c8fd36f39e29af +DIST picard-1.103.tar.bz2 15037887 SHA256 777af2a0aadd97a2b909160774e6e0ad99cef6de7763096f10660ccbe2baca63 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca WHIRLPOOL de5a0341473174bfc7a1f1b8d1b3b6122b212a1d964dda534912347595a3da9fe2a86692959df7375896292e3f3657a9c27c2f1694fca60d48ff23192b93b098 +EBUILD picard-1.103.ebuild 1513 SHA256 cb13c4568db1f87427ab63210509bf2923256cdfbfab7a127d7b124f780fa6c0 SHA512 e731bbabeed2d16707ad900a8a271143542c3c851c4becd240d79158b2f806bf5a4faf22b7c466427c406392faefc51628be621ec5b2d429a47a716d003a66c1 WHIRLPOOL 3c1175bae6571d1d0695ad5fe2a265ff9034edc4c06eaecda5ae8986fdb83b409a5b02d0636093ce0850b9c4be2da101fc680a07707669d4b81c58013cb7deea +MISC ChangeLog 3023 SHA256 93871a990cda8fe9e0be77197112a6c54ea4486323827310de73c45d143ba53d SHA512 fbaef8ada3de1410d342ab67696c2549f0857e3119c17b78bfebd2aa8ddc0ae4123e0cc1bdd2ef674fdbd36f7ee315b87167acd448a866a095372b36de09a6c5 WHIRLPOOL 1740f06e70516e2913156fba826e0b9f365aafe49e0f762d72ca4e1324a1bd610e64fbc94b55691e22581fff0cae3cb4a598069233bd7b81c3675829b68b9db5 +MISC ChangeLog-2015 1173 SHA256 14e93cee8c7bb9d7b6bcc68969e61f79158c4eb25a56afc0ac24f942c6930b0c SHA512 4f8018322128e732a2a3129a44b823791e52552e1e0d3b7b28a70aaf5e9158bc10e720d890d52618d312b21c1672fc6fd6a9dc823afbd433d8da5eb229624ab7 WHIRLPOOL 8f5d86e04162091935675249f12ccf929e8a863bec7725c5481dc1b1cd0fe9982879de98fee8aba1a9afafa671b8c501065a21acbfdddabc94d878e8b29e0510 +MISC metadata.xml 452 SHA256 970078b6008df7fe4039ac06797a81e24e146293bfbaebc6536498bb1ed70bdb SHA512 ed6d1d46bfddc918f869d55be92079c75fd720a19b681b444e6214c94753a917e3a1621b4e4f9dbdc1a8e737e118856fb60e2d7a5dbebd6dc57ffc0391bb6eaf WHIRLPOOL 718f4ed4e8eb810120973a7dbf3538edb59adccdbc2bef647d4273541d9a14d0d8a55c5b199dabe65218b5c26adaea36a1b23c651f4071afac7e883849d70613 diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch new file mode 100644 index 000000000000..00e89b95056a --- /dev/null +++ b/sci-biology/picard/files/1.103-gentoo.patch @@ -0,0 +1,131 @@ +diff --git a/build.xml b/build.xml +index fca2271..11f4fbd 100755 +--- a/build.xml ++++ b/build.xml +@@ -52,9 +52,6 @@ + <property name="testng.verbosity" value="2"/> + <property name="test.debug.port" value="5005" /> <!-- override on the command line if desired --> + +- <property environment="env"/> +- <property name="java6.home" value="${env.JAVA6_HOME}"/> +- + <condition property="isUnix"> + <os family="unix"/> + </condition> +@@ -78,9 +75,6 @@ + <pathelement location="${classes}"/> + </path> + +- <path id="java6.lib.ref"> +- <fileset dir="${java6.home}/lib" includes="*.jar"/> +- </path> + </target> + + <!-- CLEAN --> +@@ -94,10 +88,6 @@ + </target> + + <!-- COMPILE --> +- <target name="compile" depends="compile-src, compile-tests" +- description="Compile files without cleaning"> +- </target> +- + <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/> + + <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning"> +@@ -138,7 +128,7 @@ + </target> + + <!-- TEST --> +- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests"> ++ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests"> + <taskdef resource="testngtasks" classpathref="classpath"/> + <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}" + failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}" +@@ -151,6 +141,8 @@ + <classfileset dir="${classes.test}"> + <include name="**/Test*.class"/> + <include name="**/*Test.class"/> ++ <exclude name="**/ValidateSamFileTest.class" /> ++ <exclude name="**/VCFWriterUnitTest.class" /> + </classfileset> + <jvmarg value="-Xmx2G"/> + </testng> +@@ -165,7 +157,7 @@ + </target> + + <target name="single-test" +- depends="compile, compile-tests" ++ depends="compile-tests" + description="Compile and run a single test."> + <taskdef resource="testngtasks" classpathref="classpath"/> + <fail unless="name" message="Please provide input test: -Dname=..." /> +@@ -200,13 +192,12 @@ + </jar> + </target> + +- <target name="picard-jar" depends="compile" ++ <target name="picard-jar" depends="compile-src" + description="Builds picard-${picard-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/picard-${picard-version}.jar" compress="no"> + <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/> + <fileset dir="${src.scripts}" includes="**/*.R"/> +- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/> + <manifest> + <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/> + <attribute name="Implementation-Vendor" value="Broad Institute"/> +@@ -214,7 +205,7 @@ + </jar> + </target> + +- <target name="tribble-jar" depends="compile" ++ <target name="tribble-jar" depends="compile-src" + description="Builds tribble-${tribble-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no"> +@@ -225,7 +216,7 @@ + </copy> + </target> + +- <target name="variant-jar" depends="compile" ++ <target name="variant-jar" depends="compile-src" + description="Builds variant-${variant-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/variant-${variant-version}.jar" compress="no"> +@@ -262,7 +253,7 @@ + </javadoc> + </target> + +- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar"> ++ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar"> + <delete dir="${command_tmp}"/> + + <mkdir dir="${command_tmp}"/> +@@ -344,7 +335,7 @@ + </target> + + <!-- ALL --> +- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> ++ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> + <zip zipfile="${dist}/picard-tools-${picard-version}.zip"> + <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> + <zipfileset dir="${lib}" includes="snappy*.jar"/> +@@ -468,8 +459,6 @@ + target="${javac.target}"> + <classpath refid="@{compile.classpath}"/> + <compilerarg line="@{compiler.args}" /> +- <!-- ensure that Java 6 bootclasspath is used --> +- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> + </javac> + </sequential> + </macrodef> +@@ -494,8 +483,6 @@ + <pathelement location="${classes}"/> + </classpath> + <compilerarg line="@{compiler.args}"/> +- <!-- ensure that Java 6 bootclasspath is used --> +- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> + </javac> + </sequential> + </macrodef> diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml new file mode 100644 index 000000000000..513e8631c4c2 --- /dev/null +++ b/sci-biology/picard/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>ercpe@gentoo.org</email> + <name>Johann Schmitz (ercpe)</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">picard</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild new file mode 100644 index 000000000000..7a6111c87746 --- /dev/null +++ b/sci-biology/picard/picard-1.103.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +JAVA_PKG_IUSE="doc source test" +WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java-based command-line utilities that manipulate SAM files" +HOMEPAGE="http://picard.sourceforge.net/" +SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-java/snappy:1.0 + dev-java/cofoja:0 + dev-java/commons-jexl:2 + dev-java/ant-core:0" + +DEPEND=">=virtual/jdk-1.6 + dev-java/ant-apache-bcel:0 + test? ( + dev-java/testng:0 + dev-lang/R + ) + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.6 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_TEST_TARGET="test" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" +EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" + +java_prepare() { + mkdir "${S}"/lib || die + + epatch "${FILESDIR}"/${PV}-gentoo.patch + + mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die +} + +src_install() { + cd dist || die + + for i in *-${PV}.jar; do + java-pkg_newjar $i ${i/-${PV}/} + rm $i || die + done + + java-pkg_dojar *.jar + for i in *.jar; do + java-pkg_dolauncher ${i/.jar/} --jar $i; + done + + use source && java-pkg_dosrc "${S}"/src/java/* + use doc && java-pkg_dojavadoc "${S}"/javadoc +} + +src_test() { + java-pkg-2_src_test +} diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest new file mode 100644 index 000000000000..fd1a64fd3886 --- /dev/null +++ b/sci-biology/piler/Manifest @@ -0,0 +1,7 @@ +AUX piler-1.0-fix-build-system.patch 685 SHA256 d17834ccd3cbd1293889e7e45d00c52f9e9c443f7503e402185d6ffffd01c05d SHA512 e8a618615ce62aa6b4d7e5d0a4ec3facd13b6baf2573323a2f9c03d81171f1c32686bd7b82c4576e0b38cc3b30b201750034ab160cdb9170215ff480eb72a3a2 WHIRLPOOL f8965dbba5a91c28d41d00ab9576e1c198d1cf7eb76172e3baa14f18c70797e50f1fda29f429d255f350098bdae6945759ef7498dfdcc2dfd1d5c261b4ed607d +AUX piler-1.0-glibc-2.10.patch 386 SHA256 46710d6d09df3eb0cd138f70df8cc522b4c7ea4cdd94ad5153800bdfb0019dfb SHA512 0773c9b6c2eb289c8dee3cc8db6ec0250cd8df3b9e5e729305b58b28db64f486571f2f54041c84d178bf984cedfb4d9941c5abd47f772ecdf29e9ec0bdb55fcc WHIRLPOOL 363f26c862cd13d44b68694ddf8fdc85ce7b846258432f59880b951c154e32b68d0e86078b67d6d9ec7b472adc66fd9a196df0e40f6293e2dcda018645880aa9 +DIST piler-1.0.tar.gz 35220 SHA256 2940530c0afd7e49ca6e9cd8a1e3fd9890d87c71f9c19a42b1e468add83ccc69 SHA512 35be1b445f1eaf26f96d0356a04d985fb528754677403df2061c0872107d31819c5fb355e7f616e953a997e67ce781846acaf3cc2a016097aca785b6a26de3d4 WHIRLPOOL 9533cbbf7f69d5022743bb4373bbd7fea65a8a7f4657b6eb2149bf861bd920b80c1a68599820007fcf302f3d651ee2eac1266d0130ecb49714835286afb3d5c3 +EBUILD piler-1.0-r1.ebuild 660 SHA256 1da2822f5328bcda50d4f3dfdb6e4dd0386bf4e762655e92cce498b5bd8ab294 SHA512 7a8b1c64559477101989e3a97eb8d0aa3b6e520df66b0f43a97f2531a2de7fa77acb6b9e6066ab0ac46668cd23bfa9357cebbeb5c610e67f3d757e53e5ce97cf WHIRLPOOL 43919a89e8872e4cc43366af233c3b79b44487aa55ac5452de7c113bc0452e5e8d5768fa766c37e61053ff14f4e991f93119d1336b4d72f2e1330a88e9483372 +MISC ChangeLog 2455 SHA256 46bba3bbc2788f8ed31047c946e5e9d2c92a5ac33862517da591c572a9a88c08 SHA512 bc83204e51c629c021a2172970a17cebb47db222d1fef1339f0119bde943d6a1b9eae425018cccde0f86b2c080ef119ecd670e518770a0b1911bac936cf9ac66 WHIRLPOOL 031a15918c4129fefb357a684363cfc91eb5fcdced21de34ff1744d3520caad8704731dd47461cf7fb24f6e963386750ccedca6b921cde24981f3c603810646a +MISC ChangeLog-2015 995 SHA256 4855125210fca3a29776cc9f9a5b2d9d594b41fd8ff4106ea9069b8aee995668 SHA512 6fd45ade79d1988b90c20bad113867808d78ca27382c75b509d69cbffa11cc776d70f4ca5c2aba2f2de2ffef0a892e37b3ca72d75f20e08eb218af499031a00e WHIRLPOOL 59abf16de447540babf5f7cfdf94241513ce402e0d3e7488ae567828d05d09560c7687b9fa2d44d432fe8d2f8d4562c8ecc51dcead5e824dc68b6bf5f25bd257 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/piler/files/piler-1.0-fix-build-system.patch b/sci-biology/piler/files/piler-1.0-fix-build-system.patch new file mode 100644 index 000000000000..78a72f1b4850 --- /dev/null +++ b/sci-biology/piler/files/piler-1.0-fix-build-system.patch @@ -0,0 +1,34 @@ +Make build system honour user variables + +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,4 @@ +-CFLAGS = -O3 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -Winline -DNDEBUG=1 +-LDLIBS = -lm -static +-# LDLIBS = -lm ++LDLIBS = -lm + + OBJ = .o + EXE = +@@ -8,18 +6,13 @@ + RM = rm -f + CP = cp + +-GPP = g++ +-LD = $(GPP) $(CFLAGS) +-CPP = $(GPP) -c $(CFLAGS) +-CC = gcc -c $(CFLAGS) +- + all: piler + + CPPSRC = $(sort $(wildcard *.cpp)) + CPPOBJ = $(subst .cpp,.o,$(CPPSRC)) + +-$(CPPOBJ): %.o: %.cpp +- $(CPP) $< -o $@ ++%.o: %.cpp ++ $(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@ + + piler: $(CPPOBJ) +- $(LD) -o piler $(CPPOBJ) $(LDLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o piler $(CPPOBJ) $(LDLIBS) diff --git a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch new file mode 100644 index 000000000000..4c7f124c5e3d --- /dev/null +++ b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch @@ -0,0 +1,12 @@ +diff -ur piler.orig/gff.cpp piler/gff.cpp +--- piler.orig/gff.cpp 2004-12-18 01:25:29.000000000 +0200 ++++ piler/gff.cpp 2009-08-09 17:22:33.000000000 +0300 +@@ -70,7 +70,7 @@ + const char *Attrs = Fields[8];
+
+ // Truncate attrs if comment found
+- char *Pound = strchr(Attrs, '#');
++ char *Pound = const_cast <char*> (strchr(Attrs, '#'));
+ if (0 != Pound)
+ *Pound = 0;
+
diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/piler/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/piler/piler-1.0-r1.ebuild b/sci-biology/piler/piler-1.0-r1.ebuild new file mode 100644 index 000000000000..276ee9bc873e --- /dev/null +++ b/sci-biology/piler/piler-1.0-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Analysis of repetitive DNA found in genome sequences" +HOMEPAGE="http://www.drive5.com/piler/" +SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND="" +RDEPEND=" + || ( + sci-biology/muscle + sci-libs/libmuscle + ) + sci-biology/pals" + +S=${WORKDIR} + +PATCHES=( + "${FILESDIR}"/${PN}-1.0-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0-glibc-2.10.patch +) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin piler +} diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest new file mode 100644 index 000000000000..62051e7c76c4 --- /dev/null +++ b/sci-biology/pilercr/Manifest @@ -0,0 +1,7 @@ +AUX pilercr-1.0-fix-build-system.patch 673 SHA256 4f33e868c973bbc6b787ed4618574e92562a927382908f123ecd7cde0fe546ef SHA512 b744c3fdc6e1ec152a27592ce8036de080c113b6385c5743dfca325ae8e0435d34418ca9f51830c540cf8efae710d842b89dd1b2b7b772379a4f527a72ff2c06 WHIRLPOOL a011e5302a3d46de49e2263273c50a367b7bebfec25305b11cf325963933d01e033d7e965787dd597e826bb4b94fbee1aed53e80572c4dce2734aad0bd7997d5 +AUX pilercr-1.0-gcc43.patch 854 SHA256 ee86cf9ad7ab5f18f9d06673c930d4c72f1e387c5b5fccc81044edbf613d7123 SHA512 7e83a1c29f2b6b11e101ffebf99516c9da06f7fa7645aa619a89c365dc89d6ea2659d4610eea25b6e260328b56320e6d720f3d0d67a01aae450104fc9513d58e WHIRLPOOL 721e2a8207631e96adb1b9a3c638b0306f2364fae763a68d6fc9b64bfc4971803ae7c15f300116a6146d9634ced1b5d73c82923ebdde7d30d010c37dc4f32daa +DIST pilercr-1.0.tar.gz 1709144 SHA256 75f58d58567c478e271c4c554071a7d6d642e6daef8981ee2618daa7b53fa923 SHA512 c262ceef1d1af9e71f454809e940c2ad6d835a8404daa51ccef698b8348a504c697f5b5c268ec24df611f5adda2932e4982bcdabe4fbdf99d8c204f0f77f1be5 WHIRLPOOL 31639d51cb219efb62a70e05fe7be9d8e3c1980fdb11dfe6c32248f962881403a95553623de6f4a0f93897f6cc41e0344f355079a0ff2c386afa5e6d275f3304 +EBUILD pilercr-1.0-r1.ebuild 594 SHA256 4be488e3f5002392c3b0ee4c9cb0601b22a867054ed1155015cb43dbca8f6046 SHA512 5841ff12c7fa7d2290b2310aaba5fd0ec2688e5364e0f973314d9eeb6641fe43d0ff30374bc327f3d6152fd81476424f423841adac6d52656690d0a12090119c WHIRLPOOL 499287f2484a296ae3e993a9ab31cb8f7a4e08dce187144421d48746d33bdf950fc8e4c5f00b53fa644f5d33cab64d78c66643df2a821b6c1d71232568d5ff7f +MISC ChangeLog 2458 SHA256 ffa5ca6853f53b10817890f92a1b7fbc083638122e8c0c9f30f1b20fb0a0a126 SHA512 9cfeb9fd545d2b78de02c543d49198cf943285d8684dcdb6b6202718d43498bcd0e03255828a61af52148ef8c25a80245dfeba55c756c55dc1729d51b9b11639 WHIRLPOOL 53e05a378ba39e35a8506e7b048af29269676987d2382432a14d0f54181b120e6fff2e544bb230166d11267fa3f5d569d1dc7735ac0137f34e0b67e9b7b229f5 +MISC ChangeLog-2015 1130 SHA256 f497b5ef24802df4a8eac553ec05249f0c9cadb928192a13cf0945818eef4514 SHA512 5d7877a119a157a9fb36e772db9a4b105ee75e84865f223012519f4679a7e2261a9566a5d8ea73a0dcf1857b1281f3cbe0fb590589eac79c5d269801dc0e0c57 WHIRLPOOL fde7155161c441ba0d3a232ee87d6727d8b15236582a7ef4c5cfb9ad89fdaa8c82595c406e3b9a2bf49bdc7b95fbaa5b1ca713094bf29beb2baa5b6ffe7d544e +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch b/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch new file mode 100644 index 000000000000..3754f80a9346 --- /dev/null +++ b/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch @@ -0,0 +1,34 @@ +Make build system honour user variables + +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,4 @@ +-CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1 +-#CFLAGS = -O3 -funroll-loops -Winline +-LDLIBS = -lm -static +-# LDLIBS = -lm ++LDLIBS = -lm + + OBJ = .o + EXE = +@@ -9,17 +6,13 @@ + RM = rm -f + CP = cp + +-GPP = g++ +-LD = $(GPP) $(CFLAGS) +-CPP = $(GPP) -c $(CFLAGS) +- + all: pilercr + + CPPSRC = $(sort $(wildcard *.cpp)) + CPPOBJ = $(subst .cpp,.o,$(CPPSRC)) + +-$(CPPOBJ): %.o: %.cpp +- $(CPP) $< -o $@ ++%.o: %.cpp ++ $(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@ + + pilercr: $(CPPOBJ) +- $(LD) -o pilercr $(CPPOBJ) $(LDLIBS) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o pilercr $(CPPOBJ) $(LDLIBS) diff --git a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch new file mode 100644 index 000000000000..7b49df872e27 --- /dev/null +++ b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch @@ -0,0 +1,33 @@ +diff -dur work/multaln.h work-orig/multaln.h +--- work/multaln.h 2007-04-17 19:02:18.000000000 +0000 ++++ work-orig/multaln.h 2009-02-18 21:25:26.166333299 +0000 +@@ -6,6 +6,7 @@ + #define _CRT_SECURE_NO_DEPRECATE 1
+ #endif
+
++#include <cstring>
+ #include <vector>
+ #include <limits.h>
+ #include <ctype.h>
+diff -dur work/seqvect.h work-orig/seqvect.h +--- work/seqvect.h 2006-04-06 23:36:18.000000000 +0000 ++++ work-orig/seqvect.h 2009-02-18 21:25:26.171090246 +0000 +@@ -1,6 +1,7 @@ + #ifndef SeqVect_h
+ #define SeqVect_h
+
++#include <stdio.h>
+ #include <vector>
+ #include "seq.h"
+
+diff -dur work/tree.h work-orig/tree.h +--- work/tree.h 2006-04-05 23:52:42.000000000 +0000 ++++ work-orig/tree.h 2009-02-18 21:25:26.171090246 +0000 +@@ -1,6 +1,7 @@ + #ifndef tree_h
+ #define tree_h
+
++#include <stdlib.h>
+ #include <limits.h>
+
+ class Clust;
diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/pilercr/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pilercr/pilercr-1.0-r1.ebuild b/sci-biology/pilercr/pilercr-1.0-r1.ebuild new file mode 100644 index 000000000000..8b1abd5de7d7 --- /dev/null +++ b/sci-biology/pilercr/pilercr-1.0-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)" +HOMEPAGE="http://www.drive5.com/pilercr/" +SRC_URI="http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR} + +PATCHES=( + "${FILESDIR}"/${PN}-1.0-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0-gcc43.patch +) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest new file mode 100644 index 000000000000..5ac9f08542d4 --- /dev/null +++ b/sci-biology/plink/Manifest @@ -0,0 +1,9 @@ +AUX 1.07-flags.patch 1024 SHA256 f2427054a2ceecbe6bc4a1d435918a225e71313b454cef02b412d2be5eb3b12c SHA512 6511b08ea740819e2d17bfc2168951f94d8b9ad1165b3ee0966bed8f7a4fe7fb313b9b32994d0405f613c14656125db736757fc7f2a2dd726db4c90e9a13dd6a WHIRLPOOL 4781d59a6c5fe0ea03931a9271b30d5ff41f2a4527135730db00207996d17847cbe8b7f2a06bc628092c485524e5915689e71a0a848e602b355a8c36890f50d2 +AUX plink-1.07-gcc47.patch 1825 SHA256 f3019efb2ea2f979971777b29b449a85dc404ac06771c97adfbed61fbbbda8d9 SHA512 dba53ba4e50bd2352ad2ed604570525b77bc5698259b12f618284c999efb776485e94485a1ad90b8cc1744a0aa004435f77ceb467e1fb9e475065e084938f7fe WHIRLPOOL eb07308a1412753823a65e877a3f7ce3d3e67234d534fee896981347a8f1e37b6c01c9b66c0482f4c4488da89469911fc276bb1d89aa2fd6113bffd3925ce48b +DIST plink-1.07-src.zip 2257297 SHA256 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3 WHIRLPOOL 01e69f605e1b52c6087dd75b506a7705d3bdb8e7dfdd0158e125f4fc4d962fad70c4ec430a139029b3b4ae91b822eb10123fab062c6552b946ec96ca7caf37da +DIST plink-1.90_pre140514.zip 822157 SHA256 c6f93153d079b4b7f9ae4a51a3b4dcc7bc5ed60b408d39fce6234b98570b8ea7 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4 WHIRLPOOL ebcccc1dc0461afd973aa63313237bfd5d904543785115fa71f3af1925d8bb21da15bd0baf60e38f4da534c8c554202a7af6c642b274ca9a458fc0035c2758d2 +EBUILD plink-1.07-r1.ebuild 1152 SHA256 bc00097a7b578ff3e941ce46755b7e62b0372535246858ec3ba8887baed6f7ef SHA512 eabbb86e94276de320007cc589407800ec29b1a850664c7d3ea74e2a3355a0528c28bf2c8cb416dbcba513e6dc2fe14df3cbfa0fe6678d1029815c62c1822f21 WHIRLPOOL 5152360b69e55e5c9d1d32486e3962ecf56c81aecf13412cc2c22eeb8b9bd96b627f4d5b74fe8cd8b2dfaa369fc97f2919c6006cbfaa54e467f73430624c22ec +EBUILD plink-1.90_pre140514.ebuild 1129 SHA256 e00e7bcf3f41dcc62bf2731f198c9c747546d8d77ebb7a3426f91bdfacc74f3c SHA512 152653b04caa40c548108bb9cade22c968475faef8fd4af2627462928a6b2b364a8831bba569d467ff4a435e6fe76ce5d9862cb19da9565db1e9b974305fd0e4 WHIRLPOOL f73af35e80d6269c7cae33a10a0707f46e4aa43a9cb4acd9c28ec02eb26f7e48a9be9b27c56dd32da4927d0245ecb693e2631d77690210096c58ea83586be9a7 +MISC ChangeLog 2552 SHA256 28a2d8ce7d952a34d2ed8f22e028af25711458c81f2fd449f2058459019c43de SHA512 fc18513555a36255f0e2f8cf30451232550f530c6ff3f706e575a22b7b2be770e924a533fee67d6f2b9f4e996fd5aa231ceb151f247b81c17d9dae6f641e539f WHIRLPOOL f3645112f085ef3fca70324a8c9d6d7973a2b4c62bb68ac6fd9eeb197b9ebb61cf1c8d1d0e83a493cfa5e0bd7770ffda89b20eff78fe10ad63623069c4ca33a8 +MISC ChangeLog-2015 1750 SHA256 b79a87d58ae9d9a8eeaa8bd9c5c6493fc00077f0529defefa109013a5acf1c12 SHA512 382a66511906608ee6ff0890aa8a485613046440f98e78e10646818ad3ace687e83d71687c3e626667c422a9416718657e41278ea1c5bee84d6fa0d46d11e33c WHIRLPOOL 13c54f79b657f444ac22d06b61ae269f8bba84e8f3305c85b0805bc40cef2fdeb4ddda9e0d69832a20bdff068b2109ec766d576fad06b4b23f8df37f550e804b +MISC metadata.xml 437 SHA256 9e93528414a2dcaba5f262138f36e5abe247d71c74a9b457fd21f0c931b72f19 SHA512 e4161118b7560456cca5ab5f14dfcf2cd3074e6be82dac3ce45b4ccd1d9d018c210d84ce29143c384618445e0a711ab47ed5450a25662dc762e871417c0f1dd4 WHIRLPOOL 05dfae13139466092240e9477113d76056dd05c2d4a82eb32a936e59652078e6d416c4962c214a088d7f4721c09baf631610d3d8eab5c8ae5bf2f3ab632fbc65 diff --git a/sci-biology/plink/files/1.07-flags.patch b/sci-biology/plink/files/1.07-flags.patch new file mode 100644 index 000000000000..aa130f29beb2 --- /dev/null +++ b/sci-biology/plink/files/1.07-flags.patch @@ -0,0 +1,44 @@ +diff --git a/Makefile b/Makefile +index 172c795..466f09f 100644 +--- a/Makefile ++++ b/Makefile +@@ -26,25 +26,25 @@ WITH_R_PLUGINS = 1 + WITH_WEBCHECK = 1 + FORCE_32BIT = + WITH_ZLIB = 1 +-WITH_LAPACK = +-FORCE_DYNAMIC = ++WITH_LAPACK = 1 ++FORCE_DYNAMIC = 1 + + # Put C++ compiler here; Windows has it's own specific version + CXX_UNIX = g++ + CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe + + # Any other compiler flags here ( -Wall, -g, etc) +-CXXFLAGS = ++CXXFLAGS ?= -O2 + + # Misc +-LIB_LAPACK = /usr/lib/liblapack.so.3 ++LIB_LAPACK = `$(PKG_CONFIG) --libs lapack` + + + # -------------------------------------------------------------------- + # Do not edit below this line + # -------------------------------------------------------------------- + +-CXXFLAGS += -O3 -I. ++CXXFLAGS += -I. + OUTPUT = plink + + # Some system specific flags +@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o) + all : $(OUTPUT) + + $(OUTPUT) : +- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) + + $(OBJ) : $(HDR) + diff --git a/sci-biology/plink/files/plink-1.07-gcc47.patch b/sci-biology/plink/files/plink-1.07-gcc47.patch new file mode 100644 index 000000000000..6c289edae153 --- /dev/null +++ b/sci-biology/plink/files/plink-1.07-gcc47.patch @@ -0,0 +1,64 @@ + elf.cpp | 6 +++--- + idhelp.cpp | 8 ++++---- + sets.cpp | 8 ++++---- + 3 files changed, 11 insertions(+), 11 deletions(-) + +diff --git a/elf.cpp b/elf.cpp +index ec2ed3d..a57665f 100644 +--- a/elf.cpp ++++ b/elf.cpp +@@ -1175,10 +1175,10 @@ void Plink::elfBaseline() + << setw(8) << gcnt << " " + << setw(8) << (double)cnt / (double)gcnt << "\n"; + +- map<int,int>::iterator i = chr_cnt.begin(); +- while ( i != chr_cnt.end() ) ++ map<int,int>::iterator j = chr_cnt.begin(); ++ while ( j != chr_cnt.end() ) + { +- int c = i->first; ++ int c = j->first; + int x = chr_cnt.find( c )->second; + int y = chr_gcnt.find( c )->second; + +diff --git a/idhelp.cpp b/idhelp.cpp +index a9244fa..8882097 100644 +--- a/idhelp.cpp ++++ b/idhelp.cpp +@@ -772,12 +772,12 @@ void IDHelper::idHelp() + for (int j = 0 ; j < jointField.size(); j++ ) + { + set<IDField*> & jf = jointField[j]; +- set<IDField*>::iterator j = jf.begin(); ++ set<IDField*>::iterator k = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( k != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*k)->name + " " ); ++ ++k; + } + PP->printLOG(" }"); + } +diff --git a/sets.cpp b/sets.cpp +index 3a8f92f..66787e8 100644 +--- a/sets.cpp ++++ b/sets.cpp +@@ -768,11 +768,11 @@ vector_t Set::profileTestScore() + ////////////////////////////////////////////// + // Reset original missing status + +- vector<Individual*>::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector<Individual*>::iterator j = PP->sample.begin(); ++ while ( j != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*j)->missing = (*j)->flag; ++ ++j; + } + + //////////////////////////////////////////////// diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml new file mode 100644 index 000000000000..c281934d9943 --- /dev/null +++ b/sci-biology/plink/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="webcheck"> + add support for online update checking every time the program starts + </flag> + <flag name="R"> + add support R language + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/plink/plink-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild new file mode 100644 index 000000000000..3e1d4d5b0b43 --- /dev/null +++ b/sci-biology/plink/plink-1.07-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Whole genome association analysis toolset" +HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" +SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip" + +LICENSE="GPL-2" +SLOT="0" +IUSE="lapack -webcheck R" +KEYWORDS="amd64 x86" + +DEPEND=" + app-arch/unzip + lapack? ( virtual/pkgconfig )" +RDEPEND=" + sys-libs/zlib + lapack? ( virtual/lapack )" + +S="${WORKDIR}/${P}-src" + +# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian. +# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-flags.patch \ + "${FILESDIR}"/${P}-gcc47.patch + use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die + use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die + use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die + tc-export PKG_CONFIG +} + +src_compile() { + emake \ + CXX_UNIX=$(tc-getCXX) +} + +src_install() { + newbin plink p-link + dodoc README.txt +} diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild new file mode 100644 index 000000000000..9abd1604abc4 --- /dev/null +++ b/sci-biology/plink/plink-1.90_pre140514.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Whole genome association analysis toolset" +HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" +SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + app-arch/unzip + virtual/pkgconfig" +RDEPEND=" + sys-libs/zlib + virtual/cblas + virtual/lapack + " + +S="${WORKDIR}/" + +# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian. +# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. + +src_prepare() { + sed \ + -e 's:zlib-1.2.8/zlib.h:zlib.h:g' \ + -i *.{c,h} || die + + sed \ + -e 's:g++:$(CXX):g' \ + -e 's:gcc:$(CC):g' \ + -e 's:gfortran:$(FC):g' \ + -i Makefile || die + tc-export PKG_CONFIG +} + +src_compile() { + emake \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \ + BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)" +} + +src_install() { + newbin plink p-link +} diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest new file mode 100644 index 000000000000..6851a54f2a38 --- /dev/null +++ b/sci-biology/poa/Manifest @@ -0,0 +1,6 @@ +AUX 2-respect-flags.patch 743 SHA256 12178e90b6ed7a70e6d436f0ad391e151b2b0a5b36d31133016acc6a6bbded6c SHA512 496415d501040057155ba2ba261564fc00dc764626c8d41081f5463b0b40f9eae978bb8a81db15cf90f193c4ca9fe8725a2876ed175e15d37a983196b70e192f WHIRLPOOL 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fc0da5a6f4a5a4e1bc83c12cfb5c1616f839e9d71bb61daf2749b7d26ef0c576ce46073f11382602a0bce24f1ab31816b08961b75824f5175c8386b10fdf0776 diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch new file mode 100644 index 000000000000..bdd638cf64b7 --- /dev/null +++ b/sci-biology/poa/files/2-respect-flags.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index a65bed0..713a7ab 100644 +--- a/Makefile ++++ b/Makefile +@@ -26,9 +26,10 @@ LIBOBJECTS= \ + stringptr.o + + +-CC = gcc ++CC ?= gcc + #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. +-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++OPT_CFLAGS = -g ++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. + # -I$(HOME)/lib/include + # -DREPORT_MAX_ALLOC + +@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS) + + # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!! + poa: $(OBJECTS) liblpo.a +- $(CC) -o $@ $(OBJECTS) -lm liblpo.a ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a + + what: + @echo poa: partial-order based sequence alignment program diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml new file mode 100644 index 000000000000..229e2f246a80 --- /dev/null +++ b/sci-biology/poa/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">poamsa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild new file mode 100644 index 000000000000..c53fcd5f5f24 --- /dev/null +++ b/sci-biology/poa/poa-2-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +MY_P="${PN}V${PV}" + +DESCRIPTION="Fast multiple sequence alignments using partial-order graphs" +HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/" +SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz" + +# According to SF project page +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="static-libs" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-respect-flags.patch +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + OPT_CFLAGS="${CFLAGS}" \ + poa +} + +src_install() { + dobin "${S}"/poa "${S}"/make_pscores.pl + use static-libs && dolib.a "${S}"/liblpo.a + dodoc "${S}"/README "${S}"/multidom.* + insinto /usr/share/poa + doins "${S}"/*.mat +} + +pkg_postinst() { + elog "poa requires a score matrix as the first argument." + elog "This package installs two examples to ${EROOT}usr/share/poa/." +} diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest new file mode 100644 index 000000000000..3392278b624a --- /dev/null +++ b/sci-biology/prank/Manifest @@ -0,0 +1,6 @@ +AUX prank-140603-fix-c++14.patch 395 SHA256 e755cfc8b57ecf91cb75f5aa670206f69d6a8597bda1bb181f77e157b6e61127 SHA512 a7ac7e9e8a138a2ce103302a92e936ab1c0b15c72ac8cdb2aae26c8767e764b42b048d40c436cfd21b372ae471706852ca23b41150578bb83ebbb13a7b7ac014 WHIRLPOOL a9230b1f702970c430d8cc6641b085698472237e72f51a9ad21571bde4c54839322d7b479410952dd134fe20a5c70166e0380d94ab650a87020d71ba037ecbe1 +DIST prank.source.140603.tgz 150346 SHA256 9a48064132c01b6dba1eec90279172bf6c13d96b3f1b8dd18297b1a53d17dec6 SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7 WHIRLPOOL 5884563e6035b7e5a06b064035980e9fcee1cafcf559d86c8b9c8fc23628c7e9d1ba3e153a06f7322bb536120adcc6c8d169381f95d0a491b57836ada35a0de6 +EBUILD prank-140603.ebuild 739 SHA256 be4fbd1ac266dd6a21f792812b261a4dcff3e2371f0f6a5c7bd6de5ea60cc772 SHA512 81240472088098b2f2685e8a433a527d06a1efdb51edadc17380738700c1202097e5392ad06c13dfef2b554f08bb5a54b0b3008bd9329edb4f363e2688e62dd5 WHIRLPOOL 54d32b24c051122268373298cdee1491a96db8aa46fac6ab5f66e05a93d536b0cfe073f8546f4128eebb27c3f93113d4cefa0f53c9bfffca15aa3afbdf0119f8 +MISC ChangeLog 3119 SHA256 466c7fbdb55a4c3b9ec9d40556b1293f0920508a2638577f278e165749b359ff SHA512 3f3544bb2baa7df31c03c0e075de54abb8a686df562fbd21eb81f5a87ac25abffa3a30c9a91fda2c0b6452eb3cf6d2f1107d01f7834110de064408a42da7e1f2 WHIRLPOOL d8ff82d398b25fa8a69f4c902adb90345ba306294e7575061ae9289b888ce039676a32020ca18e67066c0bf7445c3a8b0bfa89da417f1472fc099ae78ec83952 +MISC ChangeLog-2015 1840 SHA256 d44f30b3a7725bd7b85e093058ec287dcecd0ef8896481efba6a9a15d96cb696 SHA512 87be0c60539ad6f91fd4bd1d29c3f8744ca8dfcb41b77766d2550d9649b475784f3c36690e66eca6ae2d1663e3fedc7637f3ab59f285f2322a0e2981b5322383 WHIRLPOOL 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cout<<"HMModel::alignmentModel: impossible 'as'"<<cout; ++ cout<<"HMModel::alignmentModel: impossible 'as'"<<bool(cout); + exit(-1); + } + diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml new file mode 100644 index 000000000000..8d1d75556076 --- /dev/null +++ b/sci-biology/prank/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">prank-msa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild new file mode 100644 index 000000000000..a29e425f43bf --- /dev/null +++ b/sci-biology/prank/prank-140603.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Probabilistic Alignment Kit" +HOMEPAGE="http://wasabiapp.org/software/prank/" +SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/${PN}-msa/src" +PATCHES=( "${FILESDIR}/${PN}-140603-fix-c++14.patch" ) + +src_prepare() { + sed \ + -e "s/\$(LINK)/& \$(LDFLAGS)/" \ + -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ + -i Makefile || die + default +} + +src_compile() { + emake \ + LINK="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest new file mode 100644 index 000000000000..756fda39e824 --- /dev/null +++ b/sci-biology/primer3/Manifest @@ -0,0 +1,10 @@ +AUX primer3-2.3.4-buildsystem.patch 5460 SHA256 13fa4df0026faa97b574e3de3a99183e66ab18eec883db92e9f234acafe8b3b8 SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037 WHIRLPOOL f09d952479f929d5e17abc3bb3a0313eae9d5811c3da14beb4d7111d17035f4077798b13f7b047ba7decd2b841c731373fb477f71a9b82f64906bbacf0118e2a +DIST primer3-2.3.5.tar.gz 1655871 SHA256 e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec WHIRLPOOL 321069f568fad409b31f2fd4caa36f1128523383f5b294dffc68d57a67489ee2ac17d53bedd8e36df9b688c43c06c91f47bdaf81b4fda6597d916ea06643e666 +DIST primer3-2.3.7.tar.gz 1658090 SHA256 9e37a301d2ca9e5034c9a9d4afcb3e90041f6cc44c658b63598d0ccfcb176e5e SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7 WHIRLPOOL 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b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch new file mode 100644 index 000000000000..cf47b35af502 --- /dev/null +++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch @@ -0,0 +1,148 @@ + src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------ + 1 file changed, 31 insertions(+), 30 deletions(-) + +diff --git a/src/Makefile b/src/Makefile +index 607ab45..a88adf4 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -52,15 +52,16 @@ TESTOPTS= + WINMAKE=mingw32-make + + LDLIBS = -lm +-AR = ar +-CC = gcc +-CPP = g++ +-O_OPTS = -O2 +-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ +-P_DEFINES = ++AR ?= ar ++CC ?= gcc ++CXX ?= g++ ++O_OPTS ?= ++CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__ ++P_DEFINES ?= + +-CFLAGS = $(CC_OPTS) $(O_OPTS) +-LDFLAGS = -g ++CFLAGS += $(CC_OPTS) $(O_OPTS) ++CXXFLAGS += $(CC_OPTS) $(O_OPTS) ++LDFLAGS += + # Note, for profiling, use + # make O_OPTS='-pg -O0' LDFLAGS='-g -pg' + +@@ -92,7 +93,7 @@ LIBPRIMER3 = libprimer3.a + LIBPRIMER3_DYN = libprimer3.so.1.0.0 + LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) + DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN) +-RANLIB = ranlib ++RANLIB ?= ranlib + + PRIMER_OBJECTS1=primer3_boulder_main.o\ + format_output.o\ +@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o + $(RANLIB) $@ + + $(LIBOLIGOTM_LIB): oligotm.o +- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o + + $(LIBDPAL): dpal_primer.o + $(AR) rv $@ dpal_primer.o + $(RANLIB) $@ + + $(LIBDPAL_DYN): dpal_primer.o +- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o + + $(LIBTHAL): thal_primer.o + $(AR) rv $@ thal_primer.o + $(RANLIB) $@ + + $(LIBTHAL_DYN): thal_primer.o +- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o + + $(LIBPRIMER3): libprimer3.o p3_seq_lib.o + $(AR) rv $@ libprimer3.o p3_seq_lib.o + $(RANLIB) $@ + + $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o +- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o + + $(PRIMER_EXE): $(PRIMER_OBJECTS) +- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) + + libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h +- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c ++ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c + + $(NTDPAL_EXE): ntdpal_main.o dpal.o +- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o ++ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o + + $(NTTHAL_EXE): thal_main.o thal.o +- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) + + $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM) +- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) + + $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o +- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) + + read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c + + print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c + + dpal.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c + + # We use '-ffloat-store' on windows to prevent undesirable + # precision which may lead to differences in floating point results. + thal.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c + + p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h +- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c ++ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c + + dpal_primer.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c + + thal_primer.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c + + format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c + + ntdpal_main.o: ntdpal_main.c dpal.h +- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c + + thal_main.o: thal_main.c thal.h +- $(CPP) -c $(CFLAGS) -o $@ thal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c + # We use CC_OPTS above rather than CFLAGS because + # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2 + + oligotm.o: oligotm.c oligotm.h + + primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c + + primer_test: test + diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml new file mode 100644 index 000000000000..664d9cf7d141 --- /dev/null +++ b/sci-biology/primer3/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + Primer3 picks primers for PCR reactions, considering: oligonucleotide + melting temperature, size, GC content, and primer-dimer possibilities; + PCR product size; positional constraints within the source sequence; + and miscellaneous other constraints. All of these criteria are + user-specifiable as constraints, and some are specifiable as terms in + an objective function that characterizes an optimal primer pair. + </longdescription> + <upstream> + <remote-id type="sourceforge">primer3</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/primer3/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild new file mode 100644 index 000000000000..513c7cb5a1a3 --- /dev/null +++ b/sci-biology/primer3/primer3-2.3.5.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Primer Design for PCR reactions" +HOMEPAGE="http://primer3.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="" +KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="dev-lang/perl" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch + + if [[ ${CHOST} == *-darwin* ]]; then + sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die + fi + + tc-export CC CXX AR RANLIB +} + +src_compile() { + emake -C src +} + +src_test () { + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" +} + +src_install () { + dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} + dodoc src/release_notes.txt example + insinto /opt/primer3_config + doins -r src/primer3_config/* primer3*settings.txt + dohtml primer3_manual.htm +} diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild new file mode 100644 index 000000000000..21a466681109 --- /dev/null +++ b/sci-biology/primer3/primer3-2.3.6.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Primer Design for PCR reactions" +HOMEPAGE="http://primer3.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="" +KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="dev-lang/perl" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch + + if [[ ${CHOST} == *-darwin* ]]; then + sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die + fi + + tc-export CC CXX AR RANLIB +} + +src_compile() { + emake -C src +} + +src_test () { + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" +} + +src_install () { + dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} + dodoc src/release_notes.txt example + insinto /opt/primer3_config + doins -r src/primer3_config/* primer3*settings.txt + dohtml primer3_manual.htm +} diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7.ebuild new file mode 100644 index 000000000000..d0dbc7363681 --- /dev/null +++ b/sci-biology/primer3/primer3-2.3.7.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs + +DESCRIPTION="Primer Design for PCR reactions" +HOMEPAGE="http://primer3.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="dev-lang/perl" +RDEPEND="" + +PATCHES=( "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch ) + +src_prepare() { + default + if [[ ${CHOST} == *-darwin* ]]; then + sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die + fi + + tc-export CC CXX AR RANLIB +} + +src_compile() { + emake -C src +} + +src_test () { + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" +} + +src_install () { + dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} + dodoc src/release_notes.txt example + insinto /opt/primer3_config + doins -r src/primer3_config/* primer3*settings.txt + docinto html + dodoc primer3_manual.htm +} diff --git a/sci-biology/prints/Manifest b/sci-biology/prints/Manifest new file mode 100644 index 000000000000..37fd81a19634 --- /dev/null +++ b/sci-biology/prints/Manifest @@ -0,0 +1,5 @@ +DIST prints-39.0.tar.bz2 26277011 SHA256 671f870230424014d4b104b24adb13ad5a30f1d947d9565de4943f77dccb5187 SHA512 4ea48a2a0892739ac4e32a6309922b7b4ad01f9d2f847f7c42c7e6a00e8f56bab0771d272adcaed1f85516ea93245fb8c7864762c4699023a8d85d61c012bdc7 WHIRLPOOL 73303a8d5c92e3bc3d7bded006bd681e0ae0314ce3f605a040a9532e7ac5ecdddb8aa813f9deb9c4068bd89e13a9b3d0c97336dc7bc33acf1c19b75c9370ce22 +EBUILD prints-39.0-r1.ebuild 1044 SHA256 ba43cca5e90d21d98471da5d828dcb1a8f6cc142b57753a39135674697a43897 SHA512 056458b00dbcee0f8720e1a74512ab513836d3ec762cd0b764c4fe3c2a8f450b76af21bff93e75fd37d0b00317bac7087c24032683125b26bbf9699b62f9cf9d WHIRLPOOL 2eafe2555e2579f3c7b3d4df2545a3fddd58c4e41ac43174fc9146412573d31ef72802908b22182a988947f07baab9086da9c7c6c74e9e61cbcb1593a7a71743 +MISC ChangeLog 2425 SHA256 d90f8176a1f120ddb6b5ef217e77158928e0399948e78f7482b1670706302168 SHA512 ae273aa9d742b182cb813719d02b523261b825ca205fa0924d0c783a4b9a88db4e3d28b6223f8aecd1920feed993f0f2a892bc2b183525e40b691fdfbc24f48a WHIRLPOOL be0323995e663ce13217bdef2ed918d704a387b8e3e46a0e6200a2b96119f44fef12f1ac8448e267d2d526b144e9a7a6d99a85a4a14f9fee4aadb2ca4ba80fd3 +MISC ChangeLog-2015 3722 SHA256 32d1b64e95e19d112f9ec33111dac20dd4f6f7aaf6d08ca7866407534f27d286 SHA512 d8cc113e4ff21e5ef9dfb4ca133a918fc626c35c432cfa806a0360565235c9ec1584a41e454de5518556ec6d21be7ee5f2479e4edc965443b0a433effed2a736 WHIRLPOOL fef37869cdc2e481d9070e7dc3d7aa8039f49073517f4268ead4abf25e5042c471e964cd0396f7c293f33beff3f0e5a2de7e0434447193c67d69ff21cec52dcb +MISC metadata.xml 883 SHA256 7de53e2e1ad011a8ebb2e1a6fb20a5f493f546992d6e235b4dac0c888f2152cb SHA512 b90e950d75cdea30ce5a8e073a02b1d60d0a02512ab73979d23f6dccf591c8f74c5f98e3d62d49031b0a9b2dfbee213445a0efa890857061239379e9b3258c5f WHIRLPOOL 525bfcac5055f30d94d0624fc37cfae404839d6ea0a89a18b19c9c4fa3d2d9d54aa553810388af14d86da2a17b1a934efda98d1814ce988226c17e6250bb8037 diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml new file mode 100644 index 000000000000..af3ff0786e0c --- /dev/null +++ b/sci-biology/prints/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + A protein motif fingerprint database maintained at the University of + Manchester. A fingerprint is a group of conserved motifs used to + characterise a protein family; its diagnostic power is refined by + iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs + do not overlap, but are separated along a sequence, though they may be + contiguous in 3D-space. Fingerprints can encode protein folds and + functionalities more flexibly and powerfully than can single motifs, + full diagnostic potency deriving from the mutual context provided by + motif neighbours. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/prints/prints-39.0-r1.ebuild b/sci-biology/prints/prints-39.0-r1.ebuild new file mode 100644 index 000000000000..f9833579e71f --- /dev/null +++ b/sci-biology/prints/prints-39.0-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PV="${PV/./_}" + +DESCRIPTION="A protein motif fingerprint database" +HOMEPAGE="http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="public-domain" +SLOT="0" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emboss minimal" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir PRINTS || die + einfo + einfo "Indexing PRINTS for usage with EMBOSS" + EMBOSS_DATA="." printsextract -auto -infile prints${MY_PV}.dat || die "Indexing PRINTS failed" + einfo + fi +} + +src_install() { + dodoc README + + if ! use minimal; then + insinto /usr/share/${PN} + doins newpr.lis ${PN}${MY_PV}.{all.fasta,dat,kdat,lis,nam,vsn} + fi + + if use emboss; then + insinto /usr/share/EMBOSS/data/${PN^^} + doins -r ${PN^^}/. + fi +} diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest new file mode 100644 index 000000000000..c3e170942280 --- /dev/null +++ b/sci-biology/probcons/Manifest @@ -0,0 +1,8 @@ +AUX gcc-4.3.patch 1300 SHA256 e9669d83770557834b54268f0b4e404981b91084587d69f6492c7160c1659d6b SHA512 a1839f844cd9ce0cd7a9542c0e4abaa859ed8f4f42de1dfae01af72ceb0326019379ba17ae56d4756bbb7d649da0b5deeb624cbcd5176de8a5ab34123fb689bd WHIRLPOOL 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000000000000..37c45c03a98f --- /dev/null +++ b/sci-biology/probcons/files/gcc-4.3.patch @@ -0,0 +1,44 @@ +diff -u probcons.orig/CompareToRef.cc probcons/CompareToRef.cc +--- probcons.orig/CompareToRef.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/CompareToRef.cc 2008-04-08 16:39:41.000000000 -0700 +@@ -16,6 +16,7 @@ + #include <limits> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + +diff -u probcons.orig/FixRef.cc probcons/FixRef.cc +--- probcons.orig/FixRef.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/FixRef.cc 2008-04-08 16:39:33.000000000 -0700 +@@ -17,6 +17,7 @@ + #include <algorithm> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + +diff -u probcons.orig/Main.cc probcons/Main.cc +--- probcons.orig/Main.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/Main.cc 2008-04-08 16:39:14.000000000 -0700 +@@ -21,6 +21,7 @@ + #include <climits> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + +diff -u probcons.orig/ProjectPairwise.cc probcons/ProjectPairwise.cc +--- probcons.orig/ProjectPairwise.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/ProjectPairwise.cc 2008-04-08 16:39:25.000000000 -0700 +@@ -16,6 +16,7 @@ + #include <limits> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch new file mode 100644 index 000000000000..e07ebe1a613f --- /dev/null +++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch @@ -0,0 +1,47 @@ +diff --git a/Makefile b/Makefile +index 75fc47a..4a19140 100644 +--- a/Makefile ++++ b/Makefile +@@ -15,6 +15,8 @@ CXX = g++ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12" + + # debug mode +@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12" + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + + ################################################################################ + # 3) Dependencies +@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot + all : $(TARGETS) + + probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc +- $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm + + compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc +- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc + + fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc +- $(CXX) $(CXXFLAGS) -o fixref FixRef.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc + + project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc +- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc + + makegnuplot : MakeGnuPlot.cc +- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc + + .PHONY : clean + clean: diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch new file mode 100644 index 000000000000..1596f3b31916 --- /dev/null +++ b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch @@ -0,0 +1,15 @@ + SafeVector.h | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/SafeVector.h b/SafeVector.h +index abf4b64..9c3292e 100644 +--- a/SafeVector.h ++++ b/SafeVector.h +@@ -8,6 +8,7 @@ + #ifndef SAFEVECTOR_H + #define SAFEVECTOR_H + ++#include <cstddef> + #include <cassert> + #include <vector> + diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/probcons/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild new file mode 100644 index 000000000000..01973b88cab9 --- /dev/null +++ b/sci-biology/probcons/probcons-1.12-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_P="${PN}_v${PV/./_}" + +DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences" +HOMEPAGE="http://probcons.stanford.edu/" +SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +# Gnuplot is explicitly runtime-only, it's run using system() +RDEPEND=" + !sci-geosciences/gmt + sci-visualization/gnuplot" +DEPEND="" + +S="${WORKDIR}/${PN}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-cxxflags.patch \ + "${FILESDIR}"/gcc-4.3.patch \ + "${FILESDIR}"/${P}-gcc-4.6.patch +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin probcons project makegnuplot + # Overlap with imagemagick + newbin compare compare-probcons + dodoc README +} + +pkg_postinst() { + ewarn "The 'compare' binary is installed as 'compare-probcons'" + ewarn "to avoid overlap with other packages." + einfo "You may also want to download the user manual" + einfo "from http://probcons.stanford.edu/manual.pdf" +} diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest new file mode 100644 index 000000000000..9b0a5204df82 --- /dev/null +++ b/sci-biology/prodigal/Manifest @@ -0,0 +1,6 @@ +AUX prodigal-2.6.3-fix-build-system.patch 1004 SHA256 a591b4457c5915767f4beb8e35dc24cad27c7465fc7187d2ef7c4cb3279d884a SHA512 c96e93cbe344bbab43b03b0046b1bca5030f4a731a0b43ea4d4ee87d303502d172fc93975a9d7b907d6ea6beeb865113122e0e2cbca7d660290994bb8214a17b WHIRLPOOL d30873d8195731fa6d3e064ab29ae955c7007c6768bece16b51964678cfa339097cea3fe013bd35550710963aab20b0e8475b469b3dd6f2743cf910027e0c793 +DIST prodigal-2.6.3.tar.gz 610934 SHA256 89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541 WHIRLPOOL d218510194777a15699cde33641768b24844e2077a1f63274a9d02c0d494c0d854dbbcf638df92839acd89916af63267d8e50b307a325f2e8026023675050fec +EBUILD prodigal-2.6.3.ebuild 518 SHA256 efe4a785351a8be9cd3432dc15c41724ecf305d6fd04faa9e54ccd98773bafc8 SHA512 44048cc1a61e2e7decd5b4dda026e4b89ba54decfb1f63ad3d378c3b8ebef707b3e3c2338108186be9a3f9400bca165f3331a1f1dd668345716b15c01189a0e1 WHIRLPOOL a4a56de898c2d2808769b4d6c9483d792c5b7f62c4d9d093724bb667f82218993633274543562ebe32f5eacb77ce0e3abfa72524132382b61928245da89e1e46 +MISC ChangeLog 2849 SHA256 ef72db7ba5819079c8675ca2da4b53e194874a6ae35497bfabf03df3f1f97b17 SHA512 901c7cbff9425af0de5bda56919a98e38e453ec433772ad7848daa4a8e33ed9c2fdd73ee58c5648053a01e918c97158fc3d3180aac96b8dd907d0ae56e65cb50 WHIRLPOOL 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b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch new file mode 100644 index 000000000000..b6d92392d179 --- /dev/null +++ b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch @@ -0,0 +1,45 @@ +Fix build system to honour user variables. + +--- a/Makefile ++++ b/Makefile +@@ -19,32 +19,31 @@ + ############################################################################## + + SHELL = /bin/sh +-CC = gcc ++CC ?= gcc + +-CFLAGS += -pedantic -Wall -O3 +-LFLAGS = -lm $(LDFLAGS) ++LIBS = -lm + + TARGET = prodigal + SOURCES = $(shell echo *.c) + HEADERS = $(shell echo *.h) + OBJECTS = $(SOURCES:.c=.o) + +-INSTALLDIR = /usr/local/bin ++BINDIR = $(EPREFIX)/usr/bin + + all: $(TARGET) + + $(TARGET): $(OBJECTS) +- $(CC) $(CFLAGS) -o $@ $^ $(LFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + %.o: %.c $(HEADERS) +- $(CC) $(CFLAGS) -c -o $@ $< ++ $(CC) -Wall -pedantic $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + + install: $(TARGET) +- install -d -m 0755 $(INSTALLDIR) +- install -m 0755 $(TARGET) $(INSTALLDIR) ++ install -d -m 0755 $(DESTDIR)$(BINDIR) ++ install -m 0755 $(TARGET) $(DESTDIR)$(BINDIR) + + uninstall: +- -rm $(INSTALLDIR)/$(TARGET) ++ -rm $(DESTDIR)$(BINDIR)/$(TARGET) + + clean: + -rm -f $(OBJECTS) diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml new file mode 100644 index 000000000000..e086d08df6f7 --- /dev/null +++ b/sci-biology/prodigal/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">prodigal</remote-id> + <remote-id type="github">hyattpd/Prodigal</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/prodigal/prodigal-2.6.3.ebuild b/sci-biology/prodigal/prodigal-2.6.3.ebuild new file mode 100644 index 000000000000..db8382982284 --- /dev/null +++ b/sci-biology/prodigal/prodigal-2.6.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" +HOMEPAGE="http://prodigal.ornl.gov/" +SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="" + +S=${WORKDIR}/${P^} + +PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch ) + +src_configure() { + tc-export CC +} diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest new file mode 100644 index 000000000000..a1c2c78c4d86 --- /dev/null +++ b/sci-biology/profphd/Manifest @@ -0,0 +1,8 @@ +AUX profphd-1.0.39-perl.patch 376 SHA256 3452144a6f1dade6ab5219b757975002b617b04b1da151593e810bbd561be500 SHA512 e4004dbb835560b3a2aa140aea0ed57812ee9dc11dc18fb7b1dbdeee73bacfef3fecfd686f15fa87cde5597ddb322057d67fa61708ba3077c5449f93a0284b8e WHIRLPOOL 5fd5111f9f5075a7533b5af6e72976cab6404f36b3be3558809815553243aaad4e763e7cc1ec8e06c3c841617200c9c7396aa64c4728f6224b4879416de8f3b8 +DIST profphd-1.0.39.tar.xz 4406776 SHA256 4ff67e7b4dcb5748ee5115f1e7b9de7de6ca1c5a7982971a7147fe4ee5a5d288 SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b WHIRLPOOL 7e149f3e724ae5e727810ace6a1063708c35bb957861e4873c0763e48af5362ea50757d94c592052fec9d6e63767d036a39104a72ba6deb981c1f6023f19464e +DIST profphd-1.0.40.tar.xz 4491592 SHA256 50c85da552993758df191e3e06910fb221a156a8eaba94badf5a716b04648c5c SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 WHIRLPOOL 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Most of these are likely to be broken. + + alternative connectivity patterns (default=3) + +-=item 3 ++=item C<3> + + predict sec + acc + htm + diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/profphd/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild new file mode 100644 index 000000000000..cacbc13cbdf2 --- /dev/null +++ b/sci-biology/profphd/profphd-1.0.39.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +DESCRIPTION="Secondary structure and solvent accessibility predictor" +HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" +SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND} + dev-perl/librg-utils-perl + sci-libs/profnet + sci-libs/profphd-utils +" + +src_prepare() { + sed \ + -e '/ln -s/s:prof$:profphd:g' \ + -i src/prof/Makefile || die + epatch "${FILESDIR}"/${P}-perl.patch +} + +src_compile() { + emake prefix="${EPREFIX}/usr" +} + +src_install() { + emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install +} diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild new file mode 100644 index 000000000000..8e24cebeb5f3 --- /dev/null +++ b/sci-biology/profphd/profphd-1.0.40.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +DESCRIPTION="Secondary structure and solvent accessibility predictor" +HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" +SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND} + dev-perl/librg-utils-perl + sci-libs/profnet + sci-libs/profphd-utils +" + +src_prepare() { + sed \ + -e '/ln -s/s:prof$:profphd:g' \ + -i src/prof/Makefile || die + epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch +} + +src_compile() { + emake prefix="${EPREFIX}/usr" +} + +src_install() { + emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install +} diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest new file mode 100644 index 000000000000..2a06a8361b57 --- /dev/null +++ b/sci-biology/prosite/Manifest @@ -0,0 +1,5 @@ +DIST prosite2017_02.tar.bz2 9234253 SHA256 ad278940c7a92ca6afb0fd8202e904c81823f8cbffa3f34319c3984ad1428216 SHA512 2b8a26a44d62d17108afc43a3ab65d024f76e41ea9c9f477024700621323d2606fcaec54411e1d3f4ddad40717ad9ce3a1989ffd92220e0d3c2acf70400d2e43 WHIRLPOOL ecde335cfb4b13359318218ac0ae4273c2e7653a79efd7bf08c58ff5b4eaa6223e3189df9909d60f5357d1c2b3ca2cdc7fbe7c5c9b0e9ecdfb961b7207076c8c +EBUILD prosite-2017.02.ebuild 980 SHA256 fa593b38a0d72e6a24e9c366c50396c1f5b8a453cbf704114a4c51a6d6a3f44a SHA512 5911898bd4cb41283277dbb4cf9ada173f29bd0378af4b7f679d5415a368085d00826ee0c709195605a03b3fc4cdd96a8d9b1613e152ea0347d9ac0d8dfdef14 WHIRLPOOL 6793dfd2a05b4ea65f79120df6d60da21624d9a846f0ba561f0b7d6676d274daab86fac8e55cdd984388c2162eb63ac3900930b098c8483bfb9195064bff1bad +MISC ChangeLog 2588 SHA256 4e481073a7b36f5ebbb32129ae644d881f07642f459f460105d88dcc871421a1 SHA512 dea2c2c1338c5e5a8077f7277e636ed6420d183140448fdc37489cbcb7fc490bb5b68ab2028e7132f3ebdf1bfa3039f6b79acc418ff31d77930077e6d77fa67a WHIRLPOOL d72a2633b0b584e3f251172085a55d00cb81c055f43001fbaeb0dbbe2f157b27d4fa465c65f470feaf673074309d1b6852e36dec07034946acdeacd72adabb25 +MISC ChangeLog-2015 16628 SHA256 5d6d0fca9742214825b3f39087c4512dba2f70e9dd2f1963982d061f5b8fca87 SHA512 29f53287f954cfe4dc5e9a4bdf6a7ee6aca30075176b9660dd1039b59a55c07426edcf9992cdf790a9e55c57891230b970d35a5402eae1f21a9045d9f8026d52 WHIRLPOOL 14d198b1ad9a1c4af19a0b85af0da3f0f72ee35a66e67ba38530784ef4e1be17ab00521e723d066054547f9de850ccb36892bb00b5528a8ae5d7166147816ef9 +MISC metadata.xml 817 SHA256 e30e900a93465725045005d36918a821eac5e5dabb9c7c3c76c43c252c8056f3 SHA512 28b74af20192bc861cf78d43e55264e84473e471ce6dcdc63f30c3b64d4727cd3e8db5b4934d79ece4a3d732263393264d9085e0e53ce16649a6269a3c40f8e9 WHIRLPOOL 5e539355b00158a2147ee0e339640b11e0c4b0e4fdf778699fd3ded2e1fcbfc32fe79e476c493138460872a805401dff4eaf7c36e2031d9ac5731f20174c48f5 diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml new file mode 100644 index 000000000000..59076478066f --- /dev/null +++ b/sci-biology/prosite/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + A protein families and domains database maintained at the Swiss + Institude for Bioinformatics. It consists of biologically significant + sites, patterns and profiles that help to reliably identify to which + known protein family (if any) a new sequence belongs. PROSITE currently + contains patterns and profiles specific for more than a thousand + protein families or domains. Each of these signatures comes with + documentation providing background information on the structure and + function of these proteins. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/prosite/prosite-2017.02.ebuild b/sci-biology/prosite/prosite-2017.02.ebuild new file mode 100644 index 000000000000..b3d9ef2335fd --- /dev/null +++ b/sci-biology/prosite/prosite-2017.02.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="A protein families and domains database" +HOMEPAGE="http://prosite.expasy.org/" +SRC_URI="ftp://ftp.expasy.org/databases/prosite/old_releases/prosite${PV//./_}.tar.bz2" + +LICENSE="swiss-prot" +SLOT="0" +# Minimal build keeps only the indexed files (if applicable). +# The non-indexed database is not installed. +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emboss minimal" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +S=${WORKDIR} + +src_compile() { + if use emboss; then + mkdir PROSITE || die + einfo + einfo "Indexing PROSITE for usage with EMBOSS" + EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die "Indexing PROSITE failed" + einfo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins *.{doc,dat} + fi + + if use emboss; then + insinto /usr/share/EMBOSS/data/PROSITE + doins -r PROSITE/. + fi +} diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest new file mode 100644 index 000000000000..d97ee24d63d1 --- /dev/null +++ b/sci-biology/psipred/Manifest @@ -0,0 +1,16 @@ +AUX 3.1-Makefile.patch 1103 SHA256 de49b937edc714ba84ea2ae0900ea92b73c58048fafb8d616e8dfa44b548e927 SHA512 6e0daf4478b5b992ed1647bf653320b18cd2582ca69ebe761654bd4bd9c9c46b7de183ae84a28582cb5543603362eb7eb6c306ff562c3ec18c292d89480fd127 WHIRLPOOL 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a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb WHIRLPOOL 92b0c8af14387db54eef5ea171ffd0c096658f6922729a6a1a1836eeb14b21b1feb3cd330dfb564eb3aaa8435d18b55f4559da96fb32f666f88349a1af3fb191 +DIST psipred3.3.tar.gz 1239746 SHA256 133eef16ba4ac6ff5e10a757290ef794552833f42ed8251ff866ae56d9527c40 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e WHIRLPOOL d3883df88bde12a0f5ba6e195dc37b7104db36d16b5846b978fb045def6c4452edce4361dcced27ed36937bbd8d0e8dd4391b8592dca390941b3450e49cc5d34 +DIST psipred3.4.tar.gz 1102416 SHA256 c0eb8877313eb0564d34fc4d0e2d8d22e09d84d245e41008227560a10e64da9d SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919 WHIRLPOOL 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f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c WHIRLPOOL 37bc0912c6a71d1396489161465c690fb63d28167694d2e43553b6684c1f1f88866b2bf71f9531c7a7f41fc8ca81a6c93c2895ed498a07e3c4836f8c8bf4a34e +EBUILD psipred-3.2.1.ebuild 1109 SHA256 cdaf7bf5a39001928178ffca0f687c1d85a64ed4a3536404e08944db3ba098da SHA512 9971b494b499b494b2a764672a074573184956fad453971b7dcb962a0728493c8339e9fba484fbb0062e2436b72516035f74d363909b3b8e85ee6060061f95a0 WHIRLPOOL 871dae22f71631ddee2ebf20d339f0e6a79ca839087e2e776aa0a742ce95897674b2e050f23aac18e757aae78e79e6c86f8059482dfbf73fc884ec9f0712a451 +EBUILD psipred-3.3.ebuild 1206 SHA256 53ab24fe6a7226162ae35d4217b6568ed4e38b21d441893f15bdff8fea05edc0 SHA512 56a3c75dd285784b36d546a3722451915527ba33821d070feb16997212749b7a8a85eaa4940dee1665bc2c28bbc4968bf3d470283852e0224c2a3a01e6347188 WHIRLPOOL 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d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch new file mode 100644 index 000000000000..0c70b6868565 --- /dev/null +++ b/sci-biology/psipred/files/3.1-Makefile.patch @@ -0,0 +1,38 @@ +diff --git a/src/Makefile b/src/Makefile +index abed8af..26061fa 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,9 +6,9 @@ + #### CFLAGS Flags to pass to C compiler. + + INCDIR = . +-CC = cc ++CC ?= gcc + +-CFLAGS = -O ++CFLAGS ?= -O2 + LIBS = -lm + + all: psipred psipass2 chkparse seq2mtx pfilt +@@ -20,16 +20,16 @@ clean: + /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt + + psipred: sspred_avpred.c ssdefs.h sspred_net.h +- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred ++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred + + psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h +- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 ++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 + + chkparse: chkparse.c +- $(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse ++ $(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse + + seq2mtx: seq2mtx.c +- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx ++ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx + + pfilt: pfilt.c +- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt ++ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt diff --git a/sci-biology/psipred/files/3.1-fgets.patch b/sci-biology/psipred/files/3.1-fgets.patch new file mode 100644 index 000000000000..e58d677258e0 --- /dev/null +++ b/sci-biology/psipred/files/3.1-fgets.patch @@ -0,0 +1,13 @@ +diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c +index 4d8e5ff..0d82483 100644 +--- a/src/sspred_avpred.c ++++ b/src/sspred_avpred.c +@@ -213,7 +213,7 @@ predict(int argc, char **argv) + int getmtx(FILE *lfil) + { + int aa, i, j, naa; +- char buf[256], *p; ++ char buf[65536], *p; + + if (fscanf(lfil, "%d", &naa) != 1) + fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch new file mode 100644 index 000000000000..564e9c8a1ef9 --- /dev/null +++ b/sci-biology/psipred/files/3.1-path.patch @@ -0,0 +1,38 @@ +diff --git a/runpsipred b/runpsipred +index 4ccf44e..34dee99 100755 +--- a/runpsipred ++++ b/runpsipred +@@ -14,13 +14,13 @@ + set dbname = uniref90filt + + # Where the NCBI programs have been installed +-set ncbidir = /usr/local/bin ++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +diff --git a/runpsipred_single b/runpsipred_single +index 1f7680b..7bd5bc3 100755 +--- a/runpsipred_single ++++ b/runpsipred_single +@@ -10,10 +10,10 @@ + # NOTE: Script modified to be more cluster friendly (DTJ April 2008) + + # Where the PSIPRED V3 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V3 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch new file mode 100644 index 000000000000..ec06d141ee34 --- /dev/null +++ b/sci-biology/psipred/files/3.2-fgets.patch @@ -0,0 +1,13 @@ +diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c +index 37b1332..4f04ab6 100644 +--- a/src/sspred_avpred.c ++++ b/src/sspred_avpred.c +@@ -223,7 +223,7 @@ predict(int argc, char **argv) + int getmtx(FILE *lfil) + { + int aa, i, j, naa; +- char buf[256], *p; ++ char buf[65536], *p; + + if (fscanf(lfil, "%d", &naa) != 1) + fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/psipred/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild new file mode 100644 index 000000000000..556b98801f31 --- /dev/null +++ b/sci-biology/psipred/psipred-3.2.1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils prefix toolchain-funcs versionator + +MY_P="${PN}$(delete_all_version_separators)" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}" + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README + newdoc BLAST+/README README-blast +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild new file mode 100644 index 000000000000..16c7fbd503a0 --- /dev/null +++ b/sci-biology/psipred/psipred-3.3.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils prefix toolchain-funcs versionator + +#MY_P="${PN}$(delete_all_version_separators)" +MY_P="${PN}${PV}" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI=" + http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz + test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* + emake -C src clean +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild new file mode 100644 index 000000000000..7b71d435ae20 --- /dev/null +++ b/sci-biology/psipred/psipred-3.4.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils prefix toolchain-funcs versionator + +#MY_P="${PN}$(delete_all_version_separators)" +MY_P="${PN}${PV}" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI=" + http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz + test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + app-shells/tcsh + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* + emake -C src clean +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild new file mode 100644 index 000000000000..7b71d435ae20 --- /dev/null +++ b/sci-biology/psipred/psipred-3.5.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils prefix toolchain-funcs versionator + +#MY_P="${PN}$(delete_all_version_separators)" +MY_P="${PN}${PV}" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI=" + http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz + test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + app-shells/tcsh + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* + emake -C src clean +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest new file mode 100644 index 000000000000..98f7f4b6eb34 --- /dev/null +++ b/sci-biology/pysam/Manifest @@ -0,0 +1,6 @@ +AUX pysam-0.12-fix-buildsystem.patch 2356 SHA256 973ab655536c8d0d8e815d1a227655aeb1389d77b488bcc0a40f1cd20faed67a SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a WHIRLPOOL 7648f5fb4c2db008a2c667f12f366dfff8e8f46127580980f893da7face03dbcbe7d70c1ca8cf8595e086d7db4acd8b6339eb51ac124bfd03cba3e60ca5101c4 +DIST pysam-0.12.0.1.tar.gz 2672020 SHA256 04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d WHIRLPOOL 5bd9f29e7458cac3839aaa9703d4c5740b1268644947f31ce7d3ddd12e0ec1948611ca5228323ce9b3b8fa5a5e0623c6fa0a0e2ce7f197fdb81aa5465915af36 +EBUILD pysam-0.12.0.1.ebuild 1204 SHA256 6e6adf1e8d4641fd59a98212b62885b05a35e7851f6773952e9b21853cb69975 SHA512 cca0548e77c3c3cd10f6253cdafb7be9c2ae094490aa9dd019b7b09e5cd0f273e9a350275a35eb55d6ddce4e46cc549f7b462f5fd4b06cfa012f1344263d41a7 WHIRLPOOL 50b3df57a0617b32e1c41fe46581ca867278f675a08ce78565be45b7d6ed5f94a902075b2dc9a7eb0307f340da5e319f88c2a69e72a588339a4d8f7d3cc490e5 +MISC ChangeLog 3211 SHA256 814821b212b72f1e2a855be2286756b938d2f77e77699c0c74a6780e9bc139ed SHA512 a2d8aea3e52e94118ba0474fc1188fb2456693a610a2ce4654ceff67fea53748df8745d5b038439abf5424f085f65314721225f0cfb65b26535ae88ddf988060 WHIRLPOOL 6630495ece6d70293fde494ce8cac7411687353f32f1b0012ad5eddea4e50eb6559ec748d4c339561327119217771a8de6ec5f108ebaff9442752b4ce2927ec2 +MISC ChangeLog-2015 858 SHA256 1aebf8e09643d1ee9a87f229d0b8813617a053ce373e3e394463b9914bdc84e9 SHA512 8ad50a8a9a15a83cec9c562b3f23b1b54c15aa2c0fb0c0757fe8b6471ac4dcb17d3cc5f98d3a669def5c3882b0943358280cf1d2ef75054f558d438787d37b62 WHIRLPOOL dd094a7d3b5f6cef469f36980243a9b3c033ca39c2f89052cb67c2c46395325a78f4e8968fa449d5b48b4fc6a8d976645cddf3d313e7d499011afddb57ae3703 +MISC metadata.xml 410 SHA256 a683ef3244d84e185203d717ab774d02fbc0dad51f7b95149b3dcf6fba0347c8 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810 WHIRLPOOL 0d34249bc0ce40ce5ede763e5ff599b2de67a6d07977da6ae3498d9d35be854673e02f69d3c20449998ce169d3cf3da76472c8ed0b5ef6d16a7de3110d536c01 diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch new file mode 100644 index 000000000000..8b323a63fba5 --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch @@ -0,0 +1,63 @@ +The build system is not designed with partial out-of-source +builds in mind. This is evident by using relative includes +such as '-Isamtools' instead of proper relative or absolute +paths. + +Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670 + +--- a/setup.py ++++ b/setup.py +@@ -359,6 +359,8 @@ + + define_macros = [] + ++samtools_include_dirs = [os.path.abspath("samtools")] ++ + chtslib = Extension( + "pysam.libchtslib", + [source_pattern % "htslib", +@@ -385,7 +387,7 @@ + htslib_sources + + os_c_files, + library_dirs=htslib_library_dirs, +- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, ++ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", + extra_compile_args=extra_compile_args, +@@ -404,7 +406,7 @@ + htslib_sources + + os_c_files, + library_dirs=htslib_library_dirs, +- include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs, ++ include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", + extra_compile_args=extra_compile_args, +@@ -423,7 +425,7 @@ + htslib_sources + + os_c_files, + library_dirs=htslib_library_dirs, +- include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs, ++ include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", + extra_compile_args=extra_compile_args, +@@ -467,7 +469,7 @@ + htslib_sources + + os_c_files, + library_dirs=["pysam"] + htslib_library_dirs, +- include_dirs=["samtools", "pysam", "."] + ++ include_dirs=["pysam", "."] + samtools_include_dirs + + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", +@@ -482,7 +484,7 @@ + htslib_sources + + os_c_files, + library_dirs=["pysam"] + htslib_library_dirs, +- include_dirs=["bcftools", "pysam", "."] + ++ include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs + + include_os + htslib_include_dirs, + libraries=external_htslib_libraries + internal_htslib_libraries, + language="c", diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml new file mode 100644 index 000000000000..6182254bd46d --- /dev/null +++ b/sci-biology/pysam/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">pysam</remote-id> + <remote-id type="github">pysam-developers/pysam</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild new file mode 100644 index 000000000000..1f4f58fdfe29 --- /dev/null +++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.python.org/pypi/pysam" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.5*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" + +PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch ) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include + export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs + sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \ + -i cy_build.py || die + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + distutils-r1_python_prepare_all +} + +src_compile() { + # TODO + # empty compile, as the build system runs the whole build again in install + : +} diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest new file mode 100644 index 000000000000..5b764eaffe75 --- /dev/null +++ b/sci-biology/qrna/Manifest @@ -0,0 +1,8 @@ +AUX 26qrna 30 SHA256 218d879e5ef893cba33d8be7e0a6cba3f08c0a475781bbbb4c32bde6e79a32b7 SHA512 ba47d1fe1cba68ca7dce369e814a67cca24339a1ec213d206001b4f87f8939d81c7e59bc285090e5ec2cec05693f560c9c4883cae8f67891f6053d9bc69cc46b WHIRLPOOL 2a4d368c898fec40b1a48484b82e6ea29d9e95a8c99622bb45d59bb999813461314589bfeec2fa223b178837f69c04ea99bb8433a9481e91464d1357e0f29547 +AUX qrna-2.0.3c-glibc-2.10.patch 7571 SHA256 17f34c9e3087f2c9d2decd95e07663813087843a778db45c5be793c6b51bb82c SHA512 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e0ce33a4a9d7da21c498efb543aca316aaa9905e5b7cfc77a11cee41ee9875a102e51acb0f6d2024beee30e24a7a52acb53c61c21ec5f801142a9404ec20bff2 WHIRLPOOL a09962f8af5e6902b54ea42e76ba79faf21b6bd97ebf6dd380732bf7723531144a27077bcf1887b659e9248bd78d761cc96010f7773e2a62ab02ad67e563e54c +MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-biology/qrna/files/26qrna b/sci-biology/qrna/files/26qrna new file mode 100644 index 000000000000..53a90b90ed78 --- /dev/null +++ b/sci-biology/qrna/files/26qrna @@ -0,0 +1 @@ +QRNADB="/usr/share/qrna/data" diff --git a/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch new file mode 100644 index 000000000000..dfa1b2a29e94 --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch @@ -0,0 +1,328 @@ +diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c +--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300 ++++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300 +@@ -215,7 +215,7 @@ + } + + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + readline(V->f, V->sbuffer); + } +@@ -277,7 +277,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -305,7 +305,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -314,7 +314,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -323,7 +323,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -337,7 +337,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -355,7 +355,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -367,7 +367,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -389,7 +389,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -398,7 +398,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -416,7 +416,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -427,7 +427,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -460,11 +460,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -494,12 +494,12 @@ + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); + +- getline(V); /*skip title-junk line*/ ++ get_line(V); /*skip title-junk line*/ + + readLoop(0, endNBRF, V); + + while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>'))) +- getline(V); ++ get_line(V); + } + + +@@ -529,7 +529,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -549,7 +549,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -571,7 +571,7 @@ + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -598,7 +598,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -607,7 +607,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -631,7 +631,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -647,7 +647,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -658,7 +658,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -680,7 +680,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -692,7 +692,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -700,7 +700,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -732,14 +732,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -747,7 +747,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -786,7 +786,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -800,7 +800,7 @@ + SeqfilePosition(SQFILE *sqfp, long offset) + { + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -817,7 +817,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -912,7 +912,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -991,7 +991,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -1098,7 +1098,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -1204,7 +1204,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch new file mode 100644 index 000000000000..d03f650dd39e --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch @@ -0,0 +1,28 @@ +diff --git a/src/Makefile b/src/Makefile +index 1d1631b..4fa3af9 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -131,17 +131,17 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + cfgbuild: $(OBJ) cfgbuild.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.c + $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-biology/qrna/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/qrna/qrna-2.0.3c-r2.ebuild b/sci-biology/qrna/qrna-2.0.3c-r2.ebuild new file mode 100644 index 000000000000..ea79f2d548f6 --- /dev/null +++ b/sci-biology/qrna/qrna-2.0.3c-r2.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Prototype ncRNA genefinder" +HOMEPAGE="http://selab.janelia.org/software.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + dev-lang/perl + sci-biology/hmmer" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-glibc-2.10.patch + "${FILESDIR}"/${P}-ldflags.patch +) + +src_prepare() { + default + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "/^AR/s:ar:$(tc-getAR):g" \ + -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \ + -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \ + -i {src,squid,squid02}/Makefile || die + rm -v squid*/*.a || die +} + +src_compile() { + local d + for d in squid squid02 src; do + emake -C ${d} + done +} + +src_install() { + dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/* + + newdoc 00README README + dodoc -r documentation/. + + insinto /usr/share/${PN}/data + doins -r lib/. + insinto /usr/share/${PN}/demos + doins -r Demos/. + + # Sets the path to the QRNA data files + doenvd "${FILESDIR}"/26qrna +} diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest new file mode 100644 index 000000000000..4b6ea77c10ad --- /dev/null +++ b/sci-biology/raxml/Manifest @@ -0,0 +1,6 @@ +AUX raxml-7.2.6-makefile.patch 777 SHA256 0e87b5cd6375669e660ef6e3c37e51e751ea8846de6c52060f484380c28610d5 SHA512 0cc326e8fed0882c56193fef9d1c98577f2252acc4dc25e650e0806d89ded0e2911e6967272a6d101cf830cfe63a190a8f5220fd7573864f5fa60106069ad74f WHIRLPOOL 896bb8f27d458e1d555ffb462abf89f55c487e595a604b3446c579a2e95719cfdfb1911873ca2570a73c3299ef49f0c489ee0c127fcb6e1acdcf907c748459b0 +DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 WHIRLPOOL 7fe7ac66412c979d3ecca17e2c06a32566fefe7bdcf39664a0885fcdebc2b8187c222ca5e29cf2685085fba21a8aff0a2aefceec08823cab155a5f62f8b59490 +EBUILD raxml-7.2.6.ebuild 962 SHA256 e23a9d95f88de3f012243d97a65d77cd7ab833933434461293b1622b68805315 SHA512 dd75e9c82ef3a3d2c3c2813690af6ac95548842e727c7819b63054d7e982b4ea7ebfd9020c4ee7b9f80bd0b38162c5559e25a19bf5a60efd2d63e3798fae243b WHIRLPOOL 9ed05cccb01a217e74781d86fd26feebb79ea1dd5045af85c244ffe88e4b788db7703af0fb0921f3613788383138aa0c89ee246dcc2f3ac0517273c553ea3ab3 +MISC ChangeLog 2496 SHA256 3ff7f51068eae5a3ee5aac56ba24c804e27f6532686a11dc4e12dad54105ca39 SHA512 4ae95033b82f5bbbbb89759053c076181d590a50c80f94d09d4854ddbad7c8f35b56b80fc983865fdfdac7c994b54c141b973d1547c32c75f01bfe8c59aa2628 WHIRLPOOL 8b8cd0213bb17cb2c19dfeb5e3dcc76cc9d7fe9fb1be88e6553b7f209de125d18cd7e846c6b751f56b738dfd5d32bfab42d3aceafa08d13f5863c96c91d4c065 +MISC ChangeLog-2015 1843 SHA256 8e1b22930f67ae96d7d4600fcd18797548ef8fe68ac0b4a652691878517897dc SHA512 40d0f7f536b7d7fb6395fdfd443f2e960b42923145d281c5198f3dd86f3fe5afb4eb85f044be8c3222e1728ff691cb34a2684fd7b3c78f36dec0056ded4c5797 WHIRLPOOL dab6051c307797ea0d57bd74d468ef98630070c8c2b51c221437cbf568c8018abc1b567d72fc27c22c7496e8a6e419c9edd5fef7af5009374619fa5068f6c875 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch new file mode 100644 index 000000000000..ae83e2eef4e7 --- /dev/null +++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch @@ -0,0 +1,29 @@ + Makefile.gcc | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile.gcc b/Makefile.gcc +index 716b6c6..f0c1de2 100644 +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,10 +1,10 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> + +-CC = gcc ++CC ?= gcc + + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse ++CFLAGS += -D_GNU_SOURCE + + + +@@ -19,7 +19,7 @@ all : raxmlHPC + GLOBAL_DEPS = axml.h globalVariables.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) ++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + classify.o : classify.c $(GLOBAL_DEPS) + evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/raxml/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild new file mode 100644 index 000000000000..50fffc34accb --- /dev/null +++ b/sci-biology/raxml/raxml-7.2.6.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" +HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" +SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse3 +threads" + +REQUIRED_USE="cpu_flags_x86_sse3" + +# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS +DEPEND="" # mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/RAxML-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-makefile.patch + + use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3 + use threads && \ + append-cflags -D_USE_PTHREADS && \ + append-ldflags -pthread + + tc-export CC +} + +src_compile() { + emake -f Makefile.gcc +} + +src_install() { + dobin raxmlHPC +} diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest new file mode 100644 index 000000000000..a31328ae87d6 --- /dev/null +++ b/sci-biology/rebase/Manifest @@ -0,0 +1,11 @@ +DIST rebase-1701.tar.xz 120604368 SHA256 cc8cf90f874dcb179b9f7654780ff783066fa6a67fffb90d6ac08d2917fa671b SHA512 1833db9d78508bbd5317f9b42b0e8129096f1695d5a14d5e2b6043bc94091a76ac404c576ad622be4e32c46aff7975a7ec3e36c3da71ce3ce1665868ee0d77cb WHIRLPOOL 641b755b92e8aa9ca2d9a69760d0414a95f38512fa235a9856a953398d5ab0c853bb4743f6790aada1d90f968bfaa76c0651aadea842fff9700941c506a29ecd +DIST rebase-1702.tar.xz 117583312 SHA256 f010388af45a58c9f40270240c65fd5a82a1fce27b1f1eb0d1fbe4b3ffd20966 SHA512 3bba0738840b966a0a58123f265de1951428c599f3af9c581e1becec17ba3a93233a231de0673dbb2dc0bb82d54096e0eed43846967bf232f412bb785ce3b23f WHIRLPOOL 70aeede45b1795fc8cc634675381d4458b32445016139d17ac5b9951cf2ff54bbc0fa50d91bf49bbed19d250553275e3c1b15cf0de5149e36d3e1567c74031ec +DIST rebase-1703.tar.xz 122252304 SHA256 dbd5fa2751b693b1babcef9c69a6f7a9e539550aeea712c569dcc0f9a93998e3 SHA512 838bf5e09073ff8520403d955a8195298def1d792d1fd3044e7c8896c6202a0340c1e96dbe80e85c5801cd3be3ed63f19488101cca02d46cdf5f1d0521ede796 WHIRLPOOL b42693781f5faa8a2dbd15204d8f1fc2dc08fb233fa536bd3c0405799059b830c8be214d34f54e2645c8c20e7bd1359882167d175a5026a8acbea29b4f00208c +DIST rebase-1704.tar.xz 124351900 SHA256 0622cf14241a4d0d725cb149378d5b2a5aa6094968afcf3f70b8025fba1cfd6b SHA512 0e4019d41ccbae86b8cb1f6dfa4c34d3fccbe084a330f04f2fdb774186e35c761655e1619d9a90d444ea3bab0910df1b60cf9a249ee31d66a254d28dd6b32cc7 WHIRLPOOL 161f04c90c1eb290625ff0ee202f78c2b1fb9c60ac5874ca11568927e4f7ea23c6a9fed42a509b1350d0b267ecb8ffa06fa4f1d38e4da0aba28ad540ea749c6c +EBUILD rebase-1701.ebuild 1052 SHA256 272c0536c5a330de50d3be55553dc0a45adb2ad3c5d7b8c7dad3ff0c9a01e295 SHA512 f5ebc17df3c888caebc01f66e813f0482279bfa89bf5ae67ebf67fc3ca6e762246cd40b35d6713510850a63e7322916b9dd8fb88c841b82c7a1734a562df494b WHIRLPOOL f3c738c2d896c4f628c0c620da5e3d2a41a4b1cafd62a0d7f0fca90de57c505112a949f7ace0e2da7ae892708993cdfb7cbd44d5d1f07cb8247ac2ff1893d295 +EBUILD rebase-1702.ebuild 1091 SHA256 a90c8a84aa2fb0d07dd0eac72ee723468ec0cfabf50e9d035f9db32fc661e57f SHA512 6b4d6cd81f35284ecee921ca02bf524d4774cc4d9115c50bcc594124d3ef3617db9802e0577a5402ceee0f139a674492e053c532a78cbad3879987b5574c4ebf WHIRLPOOL 3033c3eaae0d96afe63f1be60fbb3cfd588ca4e05b96355f9b561032c9f5b1d08b99029de5d409ce372560e6addbb8182279c963bfa865f18ee5b32f06b00ace +EBUILD rebase-1703.ebuild 1091 SHA256 a90c8a84aa2fb0d07dd0eac72ee723468ec0cfabf50e9d035f9db32fc661e57f SHA512 6b4d6cd81f35284ecee921ca02bf524d4774cc4d9115c50bcc594124d3ef3617db9802e0577a5402ceee0f139a674492e053c532a78cbad3879987b5574c4ebf WHIRLPOOL 3033c3eaae0d96afe63f1be60fbb3cfd588ca4e05b96355f9b561032c9f5b1d08b99029de5d409ce372560e6addbb8182279c963bfa865f18ee5b32f06b00ace +EBUILD rebase-1704.ebuild 1091 SHA256 a90c8a84aa2fb0d07dd0eac72ee723468ec0cfabf50e9d035f9db32fc661e57f SHA512 6b4d6cd81f35284ecee921ca02bf524d4774cc4d9115c50bcc594124d3ef3617db9802e0577a5402ceee0f139a674492e053c532a78cbad3879987b5574c4ebf WHIRLPOOL 3033c3eaae0d96afe63f1be60fbb3cfd588ca4e05b96355f9b561032c9f5b1d08b99029de5d409ce372560e6addbb8182279c963bfa865f18ee5b32f06b00ace +MISC ChangeLog 6596 SHA256 92fb45bcb60479323913c1996d172eb43a5547d0fd9fd43e89dce08f519c4375 SHA512 66e57f9259ac4e70d5685fbf4b5492a7675c74636982120ac80233b2a20a69e6b7f190c1d6146b9b9c47078753723f84c15b256d015133fdacb26d11d57e56b9 WHIRLPOOL 12278589cdf99a99fe9e398db319bb61a316bfc7bbbb060f408e41e58a00cee012ccde3882f4f83bf799e15164911354cc0ab2965f949fbd82b9d6d0ac6e6451 +MISC ChangeLog-2015 21128 SHA256 b6ff29b80d2a0354cf85684f4fca7b0af1342cc26abd14d3662e407f06032dfa SHA512 6ad5513f3e6003749004d4f7e461b3aa5917d0d448016709d67ae918ccb07f0e03dafb8c916d525ec63f0d25fcfca659565ace4031ce7b2c8165ffc3cffb54ec WHIRLPOOL f6264e3f8ec023a70532e28820cfdd3ec877cdbbefb6fb6f67ea0953b4cf90162aa7629d145917173578920e51e2b91f42b1b23d8e8b7db8142ff1c083ba6f74 +MISC metadata.xml 914 SHA256 4969698e54e50dcb212db1f62d54339fcdaf4cd94446ad0b2b252b24e1efe1e8 SHA512 86e14836fdc2e5bbc4185e8294d471555b076701041e867d0261b15c3495b131d205e8b2dafd56b96594ea2d6c0103160958e47c9c0db340a1779c8b57a696c3 WHIRLPOOL 2df25bed339494073affa6e4cdc7fccf1f69769518f364c6607c730c788cd0cec93b8a55d00e0400e6ce8614177e0204ed2203829bbee5bd9857e4386e17b257 diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml new file mode 100644 index 000000000000..1d08046a6655 --- /dev/null +++ b/sci-biology/rebase/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + The Restriction Enzyme data BASE is a collection of information about + restriction enzymes and related proteins. It is maintained by New + England Biolabs. It contains published and unpublished references, + recognition and cleavage sites, isoschizomers, commercial availability, + methylation sensitivity, crystal and sequence data. DNA + methyltransferases, homing endonucleases, nicking enzymes, specificity + subunits and control proteins are also included. More recently, + putative DNA methyltransferases and restriction enzymes, as predicted + from analysis of genomic sequences, are also listed. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/rebase/rebase-1701.ebuild b/sci-biology/rebase/rebase-1701.ebuild new file mode 100644 index 000000000000..a680fa1783bb --- /dev/null +++ b/sci-biology/rebase/rebase-1701.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PV=${PV#1} + +DESCRIPTION="A restriction enzyme database" +HOMEPAGE="http://rebase.neb.com" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emboss minimal" + +RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" +DEPEND="${RDEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + echo; einfo "Indexing Rebase for usage with EMBOSS." + mkdir REBASE || die + EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ + -protofile proto.${MY_PV} -equivalences \ + || die "Indexing Rebase failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins withrefm.${MY_PV} proto.${MY_PV} + fi + newdoc REBASE.DOC README + if use emboss; then + insinto /usr/share/EMBOSS/data/REBASE + doins REBASE/embossre.{enz,ref,sup} + insinto /usr/share/EMBOSS/data + doins REBASE/embossre.equ + fi +} diff --git a/sci-biology/rebase/rebase-1702.ebuild b/sci-biology/rebase/rebase-1702.ebuild new file mode 100644 index 000000000000..70694cf2ca8a --- /dev/null +++ b/sci-biology/rebase/rebase-1702.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PV=${PV#1} + +DESCRIPTION="A restriction enzyme database" +HOMEPAGE="http://rebase.neb.com" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" +IUSE="emboss minimal" + +RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" +DEPEND="${RDEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + echo; einfo "Indexing Rebase for usage with EMBOSS." + mkdir REBASE || die + EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ + -protofile proto.${MY_PV} -equivalences \ + || die "Indexing Rebase failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins withrefm.${MY_PV} proto.${MY_PV} + fi + newdoc REBASE.DOC README + if use emboss; then + insinto /usr/share/EMBOSS/data/REBASE + doins REBASE/embossre.{enz,ref,sup} + insinto /usr/share/EMBOSS/data + doins REBASE/embossre.equ + fi +} diff --git a/sci-biology/rebase/rebase-1703.ebuild b/sci-biology/rebase/rebase-1703.ebuild new file mode 100644 index 000000000000..70694cf2ca8a --- /dev/null +++ b/sci-biology/rebase/rebase-1703.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PV=${PV#1} + +DESCRIPTION="A restriction enzyme database" +HOMEPAGE="http://rebase.neb.com" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" +IUSE="emboss minimal" + +RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" +DEPEND="${RDEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + echo; einfo "Indexing Rebase for usage with EMBOSS." + mkdir REBASE || die + EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ + -protofile proto.${MY_PV} -equivalences \ + || die "Indexing Rebase failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins withrefm.${MY_PV} proto.${MY_PV} + fi + newdoc REBASE.DOC README + if use emboss; then + insinto /usr/share/EMBOSS/data/REBASE + doins REBASE/embossre.{enz,ref,sup} + insinto /usr/share/EMBOSS/data + doins REBASE/embossre.equ + fi +} diff --git a/sci-biology/rebase/rebase-1704.ebuild b/sci-biology/rebase/rebase-1704.ebuild new file mode 100644 index 000000000000..70694cf2ca8a --- /dev/null +++ b/sci-biology/rebase/rebase-1704.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PV=${PV#1} + +DESCRIPTION="A restriction enzyme database" +HOMEPAGE="http://rebase.neb.com" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" +IUSE="emboss minimal" + +RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" +DEPEND="${RDEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + echo; einfo "Indexing Rebase for usage with EMBOSS." + mkdir REBASE || die + EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ + -protofile proto.${MY_PV} -equivalences \ + || die "Indexing Rebase failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins withrefm.${MY_PV} proto.${MY_PV} + fi + newdoc REBASE.DOC README + if use emboss; then + insinto /usr/share/EMBOSS/data/REBASE + doins REBASE/embossre.{enz,ref,sup} + insinto /usr/share/EMBOSS/data + doins REBASE/embossre.equ + fi +} diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest new file mode 100644 index 000000000000..f560e8f0a55f --- /dev/null +++ b/sci-biology/recon/Manifest @@ -0,0 +1,7 @@ +AUX recon-1.08-buffer-overflow.patch 290 SHA256 da8bfcd418482f8529c9709ece7136939404a2436440729ccff0481246aa97cc SHA512 d903e6a8e4b61e5f91a318313203890242aa9badbf6af69009b5a3ef6351ba6984e00cdaa7aaf744095fd79557c1a5ad96a80119248cddfde9874f4b763df11b WHIRLPOOL 7889625a0d829a877e1cbde608459ab73773bbc91d26d0daf8fd835ae4611f433df9c77bd30d5fa004ef589d2b0cac2fc4797292c5a16174223d7ec4e1cd708c +AUX recon-1.08-perl-shebangs.patch 420 SHA256 2a7cfab0cf60bf2aeba4b8f93732cbece2570c5fc035a288566692daf4a94467 SHA512 b681a0f911268ab39bc64cc35f4647a71696f3cbc4610f6fb7c061ca70406934ca2f85525578c28530431725ae9399c327a7551eb19dd46552ce5e65b2399a88 WHIRLPOOL cd2e803be5cdefbb7d340970926dee446714f687d84aca95b21c7099104ffaa45d9adcd314137ceefdec2f4621026ea41ff99156f6c8a8c78953f22f0066f6f5 +DIST RECON-1.08.tar.gz 108477 SHA256 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 WHIRLPOOL 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FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp, + + void img_charge(IPROT_t **shadow, int ct, FILE *input) { + int i=0, pos=0; +- char line[151]; ++ char line[256]; + int scan_flag; + MSP_t msp; + diff --git a/sci-biology/recon/files/recon-1.08-perl-shebangs.patch b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch new file mode 100644 index 000000000000..769fe4a93c65 --- /dev/null +++ b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch @@ -0,0 +1,19 @@ +Make Perl shebangs Prefix friendly +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/scripts/MSPCollect.pl ++++ b/scripts/MSPCollect.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + if (!@ARGV) { + die "usage: MSPCollect BLAST_output_file\n"; +--- a/scripts/recon.pl ++++ b/scripts/recon.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + $path = ""; + diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/recon/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08.ebuild new file mode 100644 index 000000000000..a96403c812be --- /dev/null +++ b/sci-biology/recon/recon-1.08.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Automated de novo identification of repeat families from genomic sequences" +HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html" +SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="examples" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl" + +S=${WORKDIR}/${P^^} + +PATCHES=( + "${FILESDIR}"/${PN}-1.08-buffer-overflow.patch + "${FILESDIR}"/${PN}-1.08-perl-shebangs.patch +) + +src_prepare() { + default + sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die +} + +src_compile() { + emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -C src +} + +src_install() { + dobin scripts/* + + exeinto /usr/libexec/${PN} + doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} + + newdoc {00,}README + + if use examples; then + insinto /usr/share/${PN} + doins -r Demos + fi +} diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest new file mode 100644 index 000000000000..7b67032b7acb --- /dev/null +++ b/sci-biology/repeatmasker-libraries/Manifest @@ -0,0 +1,5 @@ +DIST repeatmaskerlibraries-20120418.tar.gz 28059668 SHA256 7bd44a70ee33ef60ab829b4cb84a2a82a6fa923e2992071f374b7a473e4dac62 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32 WHIRLPOOL 1da932f84c591221c61177116d734d00c36c52d588bcdab73ed63e8128b9c90a63f855bf4e8e603167e059f98465460b5b2e7e00e4a724bec230d27b1b32a31a +EBUILD repeatmasker-libraries-20120418.ebuild 760 SHA256 27ca39b3dcc1fb89d56f3a4c9a05bb66876b98bb5b28a182c54d876cd5459854 SHA512 ceb9b66624d509e9c6f3750d7a51d707e7b626dc3c15fe09d84be632f68ca8d0bcbde25b9b5dde4919af2449ea25877931f751f5934e2fbe7f1db0b394ef5cc0 WHIRLPOOL 2b65a5c6a1e4303f4f30c9f2d29eff89f1c8a0cf233115c086fb04d81cf445928e4028368d3fd68161be1fe9bd65b5755bd907bda3f72c01e253322926175d8e +MISC ChangeLog 2481 SHA256 b87a2e9a00d4e02437bfff7c5e86b51278d753bf4c75710f8d81c62bca4714a3 SHA512 a9612047931160f56d157ac79b7c15556b9a05d94071a4a1d1eba23241f5917db5d6b6cb7cad650f0c1b7fcc5ec40a8c62147b64bc6e43632f35888e03d4540a WHIRLPOOL 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100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/repeatmasker-libraries/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild new file mode 100644 index 000000000000..dd8c2687a1bd --- /dev/null +++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="A special version of RepBase used by RepeatMasker" +HOMEPAGE="http://repeatmasker.org/" +SRC_URI="repeatmaskerlibraries-${PV}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/Libraries" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz" + einfo 'at http://www.girinst.org/' + einfo '(select the "Repbase Update - RepeatMasker edition" link)' + einfo 'and place it in '${DISTDIR} +} + +src_install() { + insinto /usr/share/repeatmasker/Libraries + doins "${S}"/RepeatMaskerLib.embl + dodoc README + dohtml README.html +} diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest new file mode 100644 index 000000000000..fdf427105995 --- /dev/null +++ b/sci-biology/repeatmasker/Manifest @@ -0,0 +1,5 @@ +DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL 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583ea65bfc2ac3b5016af35025b298fbc0a526585beaa5c33730459429b760af13afb3e72313c1902cd00f60f41be3f545dadf1c6a5d38da41bdb23d6096a68e WHIRLPOOL a60e3053b51f4eb83178fbb4b4c494771fa429317296c8d755b8182e22624108fff3a221fc8ee99965d6bd8df8366b0819d7886ea0c3aa3eb5c8138556d6d705 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/repeatmasker/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild new file mode 100644 index 000000000000..41c28eb17f4e --- /dev/null +++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +MY_PV=${PV//\./-} + +DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" +HOMEPAGE="http://repeatmasker.org/" +SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" + +LICENSE="OSL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + sci-biology/rmblast + sci-biology/trf + sci-biology/repeatmasker-libraries" + +S="${WORKDIR}/RepeatMasker" + +src_configure() { + sed -i -e 's/system( "clear" );//' \ + -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die + echo " +env +/usr/share/${PN} +/usr/bin +2 +/opt/rmblast/bin +Y +5" | "${S}/configure" || die "configure failed" + sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ + -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ + -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ + "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die +} + +src_install() { + exeinto /usr/share/${PN} + for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do + doexe $i || die + dosym /usr/share/${PN}/$i /usr/bin/$i || die + done + + dodir /usr/share/${PN}/lib + insinto /usr/share/${PN}/lib + doins "${S}"/*.pm || die + + insinto /usr/share/${PN} + doins -r util Matrices Libraries taxonomy.dat *.help || die + keepdir /usr/share/${PN}/Libraries + + dodoc README INSTALL *.help +} diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest new file mode 100644 index 000000000000..7895e6dfa8fd --- /dev/null +++ b/sci-biology/rmblast/Manifest @@ -0,0 +1,6 @@ +AUX rmblast-1.2-gcc47.patch 31795 SHA256 f68cee00a42ab19612430cd19c6c26fd5b4f1bea78710577e3e18b8ace82896d SHA512 2db82b02b157dd39c21d1fc459c4837741088d0d764c994094096c15ce76331f33f68e7e8498f7ea43e4979cde2fd248baf0687ac08b147d1060b54ac55b83d0 WHIRLPOOL 5a258a4f3aa66afb24faa4b2708c13e478710059757ec1a63a90c23f15b003a6366477a30349f87841f31c3131a3ef3a4de17c1df27a54da639f915efbda55fe +DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 SHA256 996be9886189364fff8ed39d4668122b2e5b8b010be47d929602416d95628eef SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 WHIRLPOOL aa3ada4297812a97614b0fe218de65d7474edfb5910e156eb09b625d45338a97b35f46876f5edf6105ead8b321a28f55ed7de2ad251bbc48ffd0cfa65ee2ac7a +EBUILD rmblast-1.2-r1.ebuild 1137 SHA256 bb0f98ca5b8018ce64d0accc5e3159318e1a509779697e9d3737d33809c0e4d2 SHA512 9b624dd651e7f8988e4ae605a737c2baaa55681e30af93627b3824004d487bc94d6a389368e465c1fa74d2783342b10a41ac8c8aabee3691099e115f62c682f6 WHIRLPOOL 122872531a394837d3ef0f90d3f6388b3bbf9c9091586c090e20b3dd384e9006e8e106d6fd132f05a284cde84e6217476b0bc9cf791c04f8a293ff47e6bd278d +MISC ChangeLog 2588 SHA256 d3533f22c01b6606101f4d4f3a16121e4600a9559a1eacb732f067e53060fb6f SHA512 d9e22ee0f79e5d54f587623811f057cffed1cd7e54b2da80be7a1dbaf6551fd6541b3f662ff1de6d11c5e64e7d2a5d97e413cbc6ec48585d1c0763124a05ed5b WHIRLPOOL 463d25b60b3b38640f18a06210c2433a3c656a78170151d19edcfe4cc0536ad01999037b2d5ed6c2fe19dba66abb84e37ba49d63dfa1620bf94fce9e6cf0dbe3 +MISC ChangeLog-2015 1184 SHA256 b0427be081124505e7b0890ae979922d5c0578eff983181ee3886850b3e6f731 SHA512 48c3c1f186306117ef9a171977984c46d9059347d5a7d481e6e610dc5f2631022d3cedcd703805dbadf00352c4847a50aa52168b8cd510ec047ef8530814a6ab WHIRLPOOL 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44 +++++- + c++/include/dbapi/driver/dbapi_object_convert.hpp | 8 +- + .../dbapi/driver/impl/dbapi_driver_utils.hpp | 2 +- + c++/include/serial/impl/stltypes.hpp | 16 ++- + c++/include/serial/iterator.hpp | 6 +- + c++/include/serial/serialbase.hpp | 8 +- + c++/include/util/bitset/bmfunc.h | 7 + + c++/include/util/linkedset.hpp | 16 +-- + c++/include/util/rangemap.hpp | 4 +- + c++/src/connect/ncbi_gnutls.c | 19 ++- + c++/src/corelib/ncbifile.cpp | 2 +- + c++/src/corelib/test_boost.cpp | 156 ++++++++++++++++++++- + c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 2 +- + c++/src/serial/stdtypes.cpp | 8 +- + 19 files changed, 269 insertions(+), 45 deletions(-) + +diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp +index a9cf850..6d90e74 100644 +--- a/c++/include/corelib/ncbiexpt.hpp ++++ b/c++/include/corelib/ncbiexpt.hpp +@@ -831,7 +831,7 @@ const TTo* UppermostCast(const TFrom& from) + exception_class(const exception_class& other) \ + : base_class(other) \ + { \ +- x_Assign(other); \ ++ this->x_Assign(other); \ + } \ + public: \ + virtual ~exception_class(void) throw() {} \ +@@ -1154,7 +1154,7 @@ public: + : TBase( other) + { + m_Errno = other.m_Errno; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp +index f45d280..f0c030d 100644 +--- a/c++/include/corelib/ncbimisc.hpp ++++ b/c++/include/corelib/ncbimisc.hpp +@@ -57,6 +57,8 @@ + * @{ + */ + ++#include <stdlib.h> ++ + #ifndef NCBI_ESWITCH_DEFINED + #define NCBI_ESWITCH_DEFINED + +diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp +index 4f83db4..815c188 100644 +--- a/c++/include/corelib/ncbiobj.hpp ++++ b/c++/include/corelib/ncbiobj.hpp +@@ -2128,7 +2128,7 @@ public: + CIRef<Interface, TThisType> ref( + dynamic_cast<Interface*>(proxy->GetLockedObject()), *this); + if (ref.NotNull()) { +- Unlock(ref.GetPointer()); ++ this->Unlock(ref.GetPointer()); + } + return ref; + } +diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp +index 0bf465a..0618d9d 100644 +--- a/c++/include/corelib/ncbistl.hpp ++++ b/c++/include/corelib/ncbistl.hpp +@@ -37,7 +37,6 @@ + + #include <common/ncbi_export.h> + +- + // Get rid of some warnings in MSVC++ 6.00 + #if (_MSC_VER >= 1200) + // too long identificator name in the debug info; truncated +@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName) + #endif + + #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP) ++# if defined(NCBI_COMPILER_GCC) && NCBI_COMPILER_VERSION >= 400 ++# include <algorithm> ++# endif + // This template is used by some stl algorithms (sort, reverse...) + // We need to have our own implementation because some C++ Compiler vendors + // implemented it by using a temporary variable and an assignment operator +@@ -174,7 +176,7 @@ template<typename Iter> + inline + void iter_swap( Iter it1, Iter it2 ) + { +- swap( *it1, * it2 ); ++ swap( *it1, *it2 ); + } + + END_STD_SCOPE +diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp +index db7054f..63e3299 100644 +--- a/c++/include/corelib/ncbistr.hpp ++++ b/c++/include/corelib/ncbistr.hpp +@@ -2583,7 +2583,7 @@ public: + : TBase(other) + { + m_Pos = other.m_Pos; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp +index 69c41f3..4cd77d3 100644 +--- a/c++/include/corelib/test_boost.hpp ++++ b/c++/include/corelib/test_boost.hpp +@@ -56,10 +56,18 @@ + # undef BOOST_AUTO_TEST_MAIN + #endif + ++#ifdef NCBI_COMPILER_MSVC ++# pragma warning(push) ++// 'class' : class has virtual functions, but destructor is not virtual ++# pragma warning(disable: 4265) ++#endif ++ ++#include <boost/version.hpp> + #include <boost/test/auto_unit_test.hpp> + #include <boost/test/floating_point_comparison.hpp> + #include <boost/test/framework.hpp> + #include <boost/test/execution_monitor.hpp> ++#include <boost/test/parameterized_test.hpp> + + #include <boost/preprocessor/tuple/rem.hpp> + #include <boost/preprocessor/repeat.hpp> +@@ -72,6 +80,7 @@ + #undef BOOST_CHECK_THROW_IMPL + #undef BOOST_CHECK_NO_THROW_IMPL + #undef BOOST_FIXTURE_TEST_CASE ++#undef BOOST_PARAM_TEST_CASE + + #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL ) \ + try { \ +@@ -109,6 +118,12 @@ catch( ... ) { \ + } \ + /**/ + ++#if BOOST_VERSION >= 104200 ++# define NCBI_BOOST_LOCATION() , boost::execution_exception::location() ++#else ++# define NCBI_BOOST_LOCATION() ++#endif ++ + #define BOOST_FIXTURE_TEST_CASE( test_name, F ) \ + struct test_name : public F { void test_method(); }; \ + \ +@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )() \ + ::framework::current_test_case().p_name \ + << "\"" << ex); \ + throw boost::execution_exception( \ +- boost::execution_exception::cpp_exception_error, ""); \ ++ boost::execution_exception::cpp_exception_error, "" \ ++ NCBI_BOOST_LOCATION() ); \ + } \ + } \ + \ +@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \ + void test_name::test_method() \ + /**/ + ++#define BOOST_PARAM_TEST_CASE( function, begin, end ) \ ++ ::NCBI_NS_NCBI::NcbiTestGenTestCases( function, \ ++ BOOST_TEST_STRINGIZE( function ), \ ++ (begin), (end) ) \ ++/**/ ++ + /// Set timeout value for the test case created using auto-registration + /// facility. + #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n) \ +@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec ) \ + } BOOST_JOIN( test_name, _timeout_spec_inst ); \ + /**/ + ++/// Automatic registration of the set of test cases based on some function ++/// accepting one parameter. Set of parameters used to call that function is ++/// taken from iterator 'begin' which is incremented until it reaches 'end'. ++/// ++/// @sa BOOST_PARAM_TEST_CASE ++#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end ) \ ++ BOOST_AUTO_TU_REGISTRAR(function) ( \ ++ BOOST_PARAM_TEST_CASE(function, begin, end)) \ ++/**/ ++ ++#define BOOST_TIMEOUT(M) \ ++ do { \ ++ static string s(M); \ ++ throw boost::execution_exception( \ ++ boost::execution_exception::timeout_error, s \ ++ NCBI_BOOST_LOCATION()); \ ++ } while (0) \ ++/**/ ++ ++ + + #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT) \ + BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL) +diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp +index 6fcde61..eddde81 100644 +--- a/c++/include/dbapi/driver/dbapi_object_convert.hpp ++++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp +@@ -67,7 +67,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +@@ -92,7 +92,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +@@ -133,7 +133,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +@@ -174,7 +174,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp +index 0792a6d..b6bd64b 100644 +--- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp ++++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp +@@ -231,7 +231,7 @@ protected: + + private: + const string& m_SPName; +- mutable impl::CConnection& m_Conn; ++ impl::CConnection& m_Conn; + }; + + +diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp +index d41ab94..7d9e3ce 100644 +--- a/c++/include/serial/impl/stltypes.hpp ++++ b/c++/include/serial/impl/stltypes.hpp +@@ -412,6 +412,7 @@ public: + typedef StlIterator TStlIterator; + typedef TypeInfoIterator TTypeInfoIterator; + typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr; ++ typedef CStlClassInfoFunctions<Container> CParent; + + static TStlIterator& It(TTypeInfoIterator& iter) + { +@@ -437,7 +438,8 @@ public: + } + static bool InitIterator(TTypeInfoIterator& iter) + { +- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); ++ TStlIterator stl_iter ++ = CParent::Get(iter.GetContainerPtr()).begin(); + if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { + void* data = &iter.m_IteratorData; + new (data) TStlIterator(stl_iter); +@@ -445,7 +447,7 @@ public: + else { + iter.m_IteratorData = new TStlIterator(stl_iter); + } +- return stl_iter != Get(iter.GetContainerPtr()).end(); ++ return stl_iter != CParent::Get(iter.GetContainerPtr()).end(); + } + static void ReleaseIterator(TTypeInfoIterator& iter) + { +@@ -466,7 +468,7 @@ public: + + static bool NextElement(TTypeInfoIterator& iter) + { +- return ++It(iter) != Get(iter.GetContainerPtr()).end(); ++ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end(); + } + static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) + { +@@ -503,7 +505,7 @@ public: + + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CParent::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + it = c->erase(it); + return it != c->end(); +@@ -511,7 +513,7 @@ public: + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CParent::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +@@ -542,7 +544,7 @@ public: + } + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CParent::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + TStlIterator erase = it++; + c->erase(erase); +@@ -551,7 +553,7 @@ public: + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CParent::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp +index 25e1193..cddb046 100644 +--- a/c++/include/serial/iterator.hpp ++++ b/c++/include/serial/iterator.hpp +@@ -491,13 +491,13 @@ protected: + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) + : m_NeedType(needType) + { +- Init(beginInfo); ++ this->Init(beginInfo); + } + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, + const string& filter) + : m_NeedType(needType) + { +- Init(beginInfo, filter); ++ this->Init(beginInfo, filter); + } + + virtual bool CanSelect(const CConstObjectInfo& object) +@@ -599,7 +599,7 @@ public: + + CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo) + { +- Init(beginInfo); ++ this->Init(beginInfo); + return *this; + } + +diff --git a/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp +index be6a4f9..d59fb25 100644 +--- a/c++/include/serial/serialbase.hpp ++++ b/c++/include/serial/serialbase.hpp +@@ -364,11 +364,15 @@ public: + // cast to object type + TObject& operator*(void) + { +- return *reinterpret_cast<TObject*>(m_Buffer); ++ TObject* ptr = static_cast<TObject*> ++ (static_cast<void*>(m_Buffer)); ++ return *ptr; + } + const TObject& operator*(void) const + { +- return *reinterpret_cast<const TObject*>(m_Buffer); ++ const TObject* ptr = static_cast<const TObject*> ++ (static_cast<const void*>(m_Buffer)); ++ return *ptr; + } + + // construct/destruct object +diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h +index 5917ee5..a8c204b 100644 +--- a/c++/include/util/bitset/bmfunc.h ++++ b/c++/include/util/bitset/bmfunc.h +@@ -37,6 +37,13 @@ For more information please visit: http://bmagic.sourceforge.net + namespace bm + { + ++bm::id_t bit_block_any_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right); ++ ++bm::id_t bit_block_calc_count_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right); + + /*! + @brief Structure with statistical information about bitset's memory +diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp +index e8bbe6e..364164b 100644 +--- a/c++/include/util/linkedset.hpp ++++ b/c++/include/util/linkedset.hpp +@@ -268,10 +268,10 @@ public: + pair<iterator, bool> ins = m_Container.insert(value); + if ( ins.second ) { + if ( ins.first == begin() ) +- insertToStart(*ins.first); ++ this->insertToStart(*ins.first); + else { + iterator prev = ins.first; +- insertAfter(*--prev, *ins.first); ++ this->insertAfter(*--prev, *ins.first); + } + } + return ins; +@@ -280,10 +280,10 @@ public: + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(*iter); ++ this->removeFromStart(*iter); + else { + iterator prev = iter; +- removeAfter(*--prev, *iter); ++ this->removeAfter(*--prev, *iter); + } + m_Container.erase(iter); + } +@@ -422,10 +422,10 @@ public: + { + iterator iter = m_Container.insert(value); + if ( iter == begin() ) +- insertToStart(get(iter)); ++ this->insertToStart(get(iter)); + else { + iterator prev = iter; +- insertAfter(get(--prev), get(iter)); ++ this->insertAfter(get(--prev), get(iter)); + } + return iter; + } +@@ -433,10 +433,10 @@ public: + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(get(iter)); ++ this->removeFromStart(get(iter)); + else { + iterator prev = iter; +- removeAfter(get(--prev), get(iter)); ++ this->removeAfter(get(--prev), get(iter)); + } + m_Container.erase(iter); + } +diff --git a/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp +index c4f5f37..56e267d 100644 +--- a/c++/include/util/rangemap.hpp ++++ b/c++/include/util/rangemap.hpp +@@ -578,7 +578,7 @@ public: + // get level + + // insert element +- TSelectMapI selectIter = insertLevel(selectKey); ++ TSelectMapI selectIter = this->insertLevel(selectKey); + pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value); + + pair<iterator, bool> ret; +@@ -640,7 +640,7 @@ public: + // insert element + iterator ret; + ret.m_Range = range_type::GetWhole(); +- ret.m_SelectIter = insertLevel(selectKey); ++ ret.m_SelectIter = this->insertLevel(selectKey); + ret.m_SelectIterEnd = this->m_SelectMap.end(); + ret.m_LevelIter = ret.m_SelectIter->second.insert(value); + return ret; +diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c +index f0242b7..8b13713 100644 +--- a/c++/src/connect/ncbi_gnutls.c ++++ b/c++/src/connect/ncbi_gnutls.c +@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = { + 0 + }; + static const int kGnuTlsCompPrio[] = { +- GNUTLS_COMP_LZO, + GNUTLS_COMP_ZLIB, + GNUTLS_COMP_NULL, + 0 +@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error) + } + + ++/*ARGSUSED*/ ++static void x_set_errno(gnutls_session_t session, int error) ++{ ++# ifdef LIBGNUTLS_VERSION_NUMBER ++# if \ ++ LIBGNUTLS_VERSION_MAJOR > 1 || \ ++ LIBGNUTLS_VERSION_MINOR > 5 || \ ++ LIBGNUTLS_VERSION_PATCH > 3 ++ gnutls_transport_set_errno(session, error); ++ return; ++# endif /*LIBGNUTLS_VERSION >= 1.5.4*/ ++# endif /*LIBGNUTLS_VERSION_NUMBER*/ ++ /*NOTREACHED*/ ++ if (error) ++ errno = error; ++} ++ ++ + static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr, + void* buf, size_t size) + { +diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp +index d751e62..fdc81c7 100644 +--- a/c++/src/corelib/ncbifile.cpp ++++ b/c++/src/corelib/ncbifile.cpp +@@ -51,8 +51,8 @@ + # include <dirent.h> + # include <pwd.h> + # include <fcntl.h> +-# include <sys/time.h> + # include <sys/mman.h> ++# include <sys/time.h> + # ifdef HAVE_SYS_STATVFS_H + # include <sys/statvfs.h> + # endif +diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp +index dfd9cc8..f93d2ca 100644 +--- a/c++/src/corelib/test_boost.cpp ++++ b/c++/src/corelib/test_boost.cpp +@@ -41,6 +41,7 @@ + #ifndef BOOST_TEST_NO_LIB + # define BOOST_TEST_NO_LIB + #endif ++#define BOOST_TEST_NO_MAIN + #include <corelib/test_boost.hpp> + + #include <boost/preprocessor/cat.hpp> +@@ -95,6 +96,7 @@ const char* kTestResultTimeout = "timeout"; + const char* kTestResultAborted = "aborted"; + const char* kTestResultSkipped = "skipped"; + const char* kTestResultDisabled = "disabled"; ++const char* kTestResultToFix = "tofix"; + + + typedef but::results_reporter::format TBoostRepFormatter; +@@ -168,14 +170,24 @@ public: + unsigned long elapsed); + virtual + void test_unit_skipped(ostream& ostr, but::test_unit const& tu); ++#if BOOST_VERSION >= 104200 ++ virtual ++ void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd, ++ boost::execution_exception const& ex); ++ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up ++ using TBoostLogFormatter::log_exception; ++#else + virtual + void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd, + but::const_string explanation); ++#endif + virtual + void log_entry_start (ostream& ostr, but::log_entry_data const& led, + log_entry_types let); + virtual + void log_entry_value (ostream& ostr, but::const_string value); ++ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up ++ using TBoostLogFormatter::log_entry_value; + virtual + void log_entry_finish (ostream& ostr); + +@@ -402,10 +414,15 @@ public: + + /// Mark test case as failed due to hit of the timeout + void SetTestTimedOut(but::test_case* tc); ++ /// Register the fact of test failure ++ void SetTestErrored(but::test_case* tc); ++ /// Check if given test is marked as requiring fixing in the future ++ bool IsTestToFix(const but::test_unit* tu); + + /// Get number of actually executed tests + int GetRanTestsCount(void); +- ++ /// Get number of tests that were failed but are marked to be fixed ++ int GetToFixTestsCount(void); + /// Get string representation of result of test execution + string GetTestResultString(but::test_unit* tu); + +@@ -415,6 +432,11 @@ public: + /// Check if user initialization functions failed + bool IsInitFailed(void); + ++ /// Check if there were any test errors ++ bool HasTestErrors(void); ++ /// Check if there were any timeouted tests ++ bool HasTestTimeouts(void); ++ + private: + typedef list<TNcbiTestUserFunction> TUserFuncsList; + +@@ -493,6 +515,8 @@ private: + TUnitsSet m_DisabledTests; + /// List of all tests which result is a timeout + TUnitsSet m_TimedOutTests; ++ /// List of all tests marked as in need of fixing in the future ++ TUnitsSet m_ToFixTests; + /// List of all dependencies for each test having dependencies + TUnitToManyMap m_TestDeps; + /// Observer to make test dependencies and look for unit's timeouts +@@ -512,12 +536,18 @@ private: + /// String representation for whole test timeout (real value taken from + /// CHECK_TIMEOUT in Makefile). + string m_TimeoutStr; ++ /// Multiplicator for timeouts ++ double m_TimeMult; + /// Timer measuring elapsed time for the whole test + CStopWatch m_Timer; + /// Timeout that was set in currently executing unit before adjustment + /// + /// @sa AdjustTestTimeout() + unsigned int m_CurUnitTimeout; ++ /// Flag showing if there were some test errors ++ bool m_HasTestErrors; ++ /// Flag showing if there were some timeouted tests ++ bool m_HasTestTimeouts; + }; + + +@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void) + m_RunMode (0), + m_DummyTest(NULL), + m_Timeout (0), +- m_Timer (CStopWatch::eStart) ++ m_TimeMult (1), ++ m_Timer (CStopWatch::eStart), ++ m_HasTestErrors(false), ++ m_HasTestTimeouts(false) + { + m_Reporter = new CNcbiBoostReporter(); + m_Logger = new CNcbiBoostLogger(); +@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void) + return result; + } + ++int ++CNcbiTestApplication::GetToFixTestsCount(void) ++{ ++ int result = 0; ++ ITERATE(TUnitsSet, it, m_ToFixTests) { ++ if (!but::results_collector.results((*it)->p_id).passed()) ++ ++result; ++ } ++ return result; ++} ++ ++inline bool ++CNcbiTestApplication::IsTestToFix(const but::test_unit* tu) ++{ ++ return m_ToFixTests.find(const_cast<but::test_unit*>(tu)) ++ != m_ToFixTests.end(); ++} ++ + inline void + CNcbiTestApplication::x_SetupBoostReporters(void) + { +@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[]) + return NULL; + } + ++inline bool ++CNcbiTestApplication::HasTestErrors(void) ++{ ++ return m_HasTestErrors; ++} ++ ++inline bool ++CNcbiTestApplication::HasTestTimeouts(void) ++{ ++ return m_HasTestTimeouts; ++} ++ + void + CNcbiTestsCollector::visit(but::test_case const& test) + { +@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu, + // elapsed comes in microseconds + if (timeout != 0 && timeout < elapsed / 1000000) { + boost::execution_exception ex( +- boost::execution_exception::timeout_error, "Timeout exceeded"); ++ boost::execution_exception::timeout_error, "Timeout exceeded" ++ NCBI_BOOST_LOCATION()); + but::framework::exception_caught(ex); + } ++ ++ but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id]; ++ if (!tr.passed() && s_GetTestApp().IsTestToFix(&tu)) { ++ static_cast<but::readwrite_property<bool>& >( ++ static_cast<but::class_property<bool>& >( ++ tr.p_skipped)).set(true); ++ static_cast<but::readwrite_property<but::counter_t>& >( ++ static_cast<but::class_property<but::counter_t>& >( ++ tr.p_assertions_failed)).set(0); ++ } + } + + void +@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu) + m_Upper->test_unit_skipped(ostr, tu); + } + ++#if BOOST_VERSION >= 104200 ++void ++CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd, ++ boost::execution_exception const& ex) ++{ ++ m_Upper->log_exception(ostr, lcd, ex); ++} ++#else + void + CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd, + but::const_string explanation) + { + m_Upper->log_exception(ostr, lcd, explanation); + } ++#endif + + void + CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led, +@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name) + END_NCBI_SCOPE + + ++using namespace but; ++ + /// Global initialization function called from Boost framework +-but::test_suite* ++test_suite* + init_unit_test_suite(int argc, char* argv[]) + { + return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv); + } ++ ++// This main() is mostly a copy from Boost's unit_test_main.ipp ++int ++main(int argc, char* argv[]) ++{ ++ int result = boost::exit_success; ++ ++ try { ++ framework::init( &init_unit_test_suite, argc, argv ); ++ ++ if( !runtime_config::test_to_run().is_empty() ) { ++ test_case_filter filter( runtime_config::test_to_run() ); ++ ++ traverse_test_tree( framework::master_test_suite().p_id, filter ); ++ } ++ ++ framework::run(); ++ ++ // Let's try to make report in case of any error after all catches. ++ //results_reporter::make_report(); ++ ++ if (!runtime_config::no_result_code()) { ++ result = results_collector.results( framework::master_test_suite().p_id ).result_code(); ++ if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors() ++ && NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts()) ++ { ++ // This should certainly go to the output. So we can use only ++ // printf, nothing else. ++ printf("There were no test failures, only timeouts.\n" ++ " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n"); ++ } ++ } ++ } ++#if BOOST_VERSION >= 104200 ++ catch( framework::nothing_to_test const& ) { ++ result = boost::exit_success; ++ } ++#endif ++ catch( framework::internal_error const& ex ) { ++ results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ catch( framework::setup_error const& ex ) { ++ results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ catch( std::exception const& ex ) { ++ results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ catch( ... ) { ++ results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ ++ results_reporter::make_report(); ++ ++ return result; ++} +diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp +index 92e817f..cfab8ab 100644 +--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp ++++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp +@@ -1199,7 +1199,7 @@ private: + CSeqDBAtlasHolder m_AtlasHolder; + + /// Reference to memory management layer. +- mutable CSeqDBAtlas & m_Atlas; ++ CSeqDBAtlas & m_Atlas; + + /// The list of database names provided to the constructor. + string m_DBNames; +diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp +index f6fa651..d6e8f80 100644 +--- a/c++/src/serial/stdtypes.cpp ++++ b/c++/src/serial/stdtypes.cpp +@@ -720,7 +720,7 @@ public: + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CParent::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -751,7 +751,7 @@ public: + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CParent::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } +@@ -786,7 +786,7 @@ public: + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CParent::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -817,7 +817,7 @@ public: + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CParent::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/rmblast/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild new file mode 100644 index 000000000000..db7c5a246910 --- /dev/null +++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +MY_NCBI_BLAST_V=2.2.23+ + +DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+" +HOMEPAGE="http://www.repeatmasker.org/RMBlast.html" +SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz" + +LICENSE="OSL-2.1" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-libs/boost" +DEPEND="${RDEPEND} + app-arch/cpio" + +S="${WORKDIR}/${P}-ncbi-blast-${MY_NCBI_BLAST_V}-src/c++" + +src_prepare() { + filter-ldflags -Wl,--as-needed + sed \ + -e 's/-print-file-name=libstdc++.a//' \ + -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ + -e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \ + -e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \ + -i src/build-system/configure || die + epatch "${FILESDIR}"/${P}-gcc47.patch +} + +src_configure() { + tc-export CXX CC + + "${S}"/configure --without-debug \ + --with-mt \ + --without-static \ + --with-dll \ + --prefix="${ED}"/opt/${PN} \ + --with-boost="${EPREFIX}/usr/include/boost" \ + || die +} diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest new file mode 100644 index 000000000000..c891931aaa3e --- /dev/null +++ b/sci-biology/rnaview/Manifest @@ -0,0 +1,7 @@ +AUX rnaview-20040713-implicit.patch 347 SHA256 129554c5ae9ed20c2cd24759b1007669c5f5ad19ddb76698c2b9157fcf79fb97 SHA512 698369b7640a36c26970649a8e0fd240c3177b3a3f7d9b8059fb6c294c39ad61389ba8a6eb3d465c3a999981fff47e2aa175ea52b38068145e2941c5934c4a0b WHIRLPOOL 5dcec3fe99bfd1efa66ecdfc55f6c553700421b0de833361fc7af3fa2654b3dd78e180d215ef1f880c1c059cad402a5ea478db23f6ee550f599ae32f5f008f43 +AUX rnaview-20040713-makefile.patch 2131 SHA256 dc2324a361132df317683a3a9d835364a7e3cff73f953920a97ca53bfc951c1a SHA512 9cde6186c0865405546bbee68ec64bd11cdfe91747b90739b237368b2724763ac4dd9206defec7f00a918449fc2a8451c3a5e447cfddfb7ca5c5fed00bb29de6 WHIRLPOOL 5f0d15d5df23d759448b763ec9c204a86658a852040c6b9e60f3dc07b37d45073c82e8ab83d0da7e2abc6bdf483b6d1258401ff0d730d24809941072aa5eba17 +DIST rnaview-20040713.tar.bz2 433916 SHA256 0961779c83e247a4b04c02d90d3850e8c4c889b630194ea1516cbeb6c6dbad17 SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e WHIRLPOOL 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5ad5c09bf14cfefa9281b88db3ea8b23365c36bc4574ef309f3745b7ca560302e8b3f98ab201ed940c123fbd1968507208b8d6655d85c4fa937518aab1404d06 WHIRLPOOL 8f795a1decab226ce65affc5234c79852bc979580dddbdc116e41182f59a8aba0231c7bea737b3d089f4db5b6eb2aa6e87128bda6daabe97df711540b9044f06 +MISC metadata.xml 666 SHA256 1449cb6570fdd20b89395441b6f7b9482202827474ba53a2a602378ac9c58a99 SHA512 70614f391a69e8f2b21d1b3a277d7693436fb8d2089e390b61a1d71ecacdadf2818f7d255a083dcb4c585df90817c5e9d129e38f365635197d74e81e84c33786 WHIRLPOOL aba4dc0921474d53184fa09237bf1ba240b50a60c65324254f112ef264b8032e939f39d1d2f849b25f6c88a1449571b171aecf20c245ea55fcd08409a3a3a7ad diff --git a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch new file mode 100644 index 000000000000..90ea72ab6f8c --- /dev/null +++ b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch @@ -0,0 +1,13 @@ +Fix implicit function declaration + +--- a/src/xml2ps.c ++++ b/src/xml2ps.c +@@ -36,7 +36,7 @@ + void read_sugar_syn(char *inpfile, long **sugar_syn); + void get_sugar_syn(FILE *inp, char *value_ch); + void get_chain_broken(long nres, double **a, double **b, long *chain_broken); +- ++extern void get_BDIR(char *BDIR, char *filename); + + + FILE *psfile; diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch new file mode 100644 index 000000000000..1af72f581fbf --- /dev/null +++ b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch @@ -0,0 +1,87 @@ + Makefile | 20 +++++++++++++++++--- + rnaml2ps/Makefile | 19 ++++++++++++------- + 2 files changed, 29 insertions(+), 10 deletions(-) + +diff --git a/Makefile b/Makefile +index 452e6c4..00d35f0 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,4 +1,4 @@ +-CC = cc ++CC ?= cc + + + +@@ -56,12 +56,17 @@ OBJ_FILE = $(OBJ)/rnaview.o \ + $(OBJ)/multiple.o \ + $(OBJ)/statistics.o + ++.PHONY: clean all install ++ ++SUBDIRS = rnaml2ps ++ + all: $(RNAVIEW) ++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} all ) ; done + +-CFLAGS = $(LINCLUDES) ++CFLAGS += $(LINCLUDES) + + $(RNAVIEW) : $(HFILES) $(OBJ_FILE) +- $(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ_FILE) -lm $(MALLOCLIB) + + + +@@ -111,6 +116,15 @@ $(OBJ)/statistics.o : $(SRC)/statistics.c + clean: + @rm -f $(OBJ)/*.o + @rm -f $(ALLTARGETS) ++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} clean ) ; done ++ ++install: ++ install -D -m 0755 bin/rnaview $(DESTDIR)/usr/bin/rnaview ++ mkdir -p $(DESTDIR)/usr/share/rnaview/BASEPARS ++ install -m 0644 BASEPARS/* $(DESTDIR)/usr/share/rnaview/BASEPARS ++ mkdir -p $(DESTDIR)/usr/share/rnaview/test ++ install -m 0644 test/* $(DESTDIR)/usr/share/rnaview/test ++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} install ) ; done + + export: + mkdir -p $(EXPORT_DIR) +diff --git a/rnaml2ps/Makefile b/rnaml2ps/Makefile +index d207655..2278ccc 100644 +--- a/rnaml2ps/Makefile ++++ b/rnaml2ps/Makefile +@@ -1,20 +1,25 @@ +-CFLAGS = -O +-CC = cc ++CFLAGS ?= -O ++CC ?= cc + + # ++++++++++++++++++++++++++++ Program RNADRAW + RNADRAW = rnaml2ps + OBJS_RNADRAW = rnaml2ps.o nrutil.o + ++all: $(RNADRAW) ++ + $(RNADRAW): $(OBJS_RNADRAW) +- $(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm ++ $(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm + + nrutil.o : nrutil.c +- cc -c nrutil.c ++ $(CC) $(CFLAGS) -c nrutil.c + + rnaml2ps.o : rnaml2ps.c +- cc -c rnaml2ps.c ++ $(CC) $(CFLAGS) -c rnaml2ps.c + + +-.PHONY : clean ++.PHONY : clean all install + clean: +- rm *.o ++ rm -f *.o ++ ++install: ++ install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW) diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml new file mode 100644 index 000000000000..cfffc1223753 --- /dev/null +++ b/sci-biology/rnaview/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + The RNAView program generates 2-dimensional displays of RNA/DNA + secondary structures with tertiary interactions. RNAView + automatically identifies and classifies the types of base pairs that + are formed in nucleic acid structures, fully implementing Leontis and + Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge + hydrogen bonding interactions. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/rnaview/rnaview-20040713-r4.ebuild b/sci-biology/rnaview/rnaview-20040713-r4.ebuild new file mode 100644 index 000000000000..729095be063c --- /dev/null +++ b/sci-biology/rnaview/rnaview-20040713-r4.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions" +HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-implicit.patch +) + +src_prepare() { + default + tc-export CC +} + +src_install() { + default + + cat > 22rnaview <<- EOF || die + RNAVIEW="${EPREFIX}/usr/share/${PN}" + EOF + doenvd 22rnaview +} diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest new file mode 100644 index 000000000000..ff022d6fcf34 --- /dev/null +++ b/sci-biology/samtools/Manifest @@ -0,0 +1,9 @@ +AUX samtools-0.1.20-buildsystem.patch 6737 SHA256 3ea8caadb8df363b5c4b21f0d6205cc5ade79bbab13070483fad5d5145323bea SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d WHIRLPOOL 469588de06a4dc81c2d2b15d7502a2419af6b42561be5935792ec13d2938e141c7fb7f2fd0d8361975157db613964ebacca9f0129ca57204a51bd09e5a82f12e +AUX samtools-1.5-buildsystem.patch 18442 SHA256 a7784c89cc06da00fa3f8470402a65a0298ef64edcb94d83694cde3cd04c16c4 SHA512 2405c9c5bd2892756dd70147d0bc57f11f869ac2b6bb12d4350e3f7145727a4c8a602489bca5dbcbe8131d52572d4573e8507a2b989ac0ac86aa8dfef92e58d4 WHIRLPOOL 54afdce038497f040e99ab6690142d9245ddb634bb11abf5f84b78d8297884d30be7073efdb09a2fc9d304a5f48ae3fe31518d171eaea16c668b7a5fce625ec8 +DIST samtools-0.1.20.tar.gz 566387 SHA256 500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 WHIRLPOOL 3ea05df172ea6afe31bd3880f918e0b286f65839f78ed846a0d3aef84ec70df1e3741ff6dcad5f70d62a06687f07b35609829aabd33c6688fac0d59effd979e0 +DIST samtools-1.5.tar.bz2 4190142 SHA256 8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6 SHA512 ff3e39ba867ecbd88f3363b038508c1557e349ea4223483f8f4ecb17ff8864fb53cd193bc2059a147e30f07395bbf53c8518d0f70219e454375c8bffe56e3059 WHIRLPOOL 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1f8c3b08c0264503a911ce0f7e0495a441f73500bed6bb36fbf0507311d491b794e547537c8ad7917dcdd3f59a4f4af3b742caa4dbbc29eaed5ed180e05944de diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch new file mode 100644 index 000000000000..eb9f6934a96f --- /dev/null +++ b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch @@ -0,0 +1,206 @@ +--- samtools-0.1.20/bcftools/Makefile ++++ samtools-0.1.20/bcftools/Makefile +@@ -1,6 +1,6 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE ++CC?= gcc ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. + AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o +@@ -11,14 +11,14 @@ + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ + + all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -31,7 +31,7 @@ + $(AR) -csru $@ $(LOBJS) + + bcftools:lib $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread + + bcf.o:bcf.h + vcf.o:bcf.h +--- samtools-0.1.20/Makefile ++++ samtools-0.1.20/Makefile +@@ -4,10 +4,10 @@ + # make git-stamp + VERSION= + +-CC= gcc +-CFLAGS= -g -Wall $(VERSION) -O2 +-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 ++CC?= gcc ++CFLAGS?= -g -Wall $(VERSION) -O2 ++#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ + bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ +@@ -28,14 +28,14 @@ + .PHONY: all lib + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -48,22 +48,22 @@ + .PHONY:all lib clean cleanlocal + .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur + +-lib:libbam.a ++lib:libbam-0.1-legacy.a + +-libbam.a:$(LOBJS) ++libbam-0.1-legacy.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + + samtools:lib-recur $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread + + bgzf.o:bgzf.c bgzf.h +- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -90,17 +90,17 @@ + faidx_main.o:faidx.h razf.h + + +-libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++libbam-0.1-legacy.1.dylib-local:$(LOBJS) ++ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz + +-libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++libbam-0.1-legacy.so.1-local:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread + + dylib: + @$(MAKE) cleanlocal; \ + case `uname` in \ +- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \ +- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \ ++ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \ ++ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \ + *) echo 'Unknown OS';; \ + esac + +--- samtools-0.1.20/misc/Makefile ++++ samtools-0.1.20/misc/Makefile +@@ -1,8 +1,8 @@ +-CC= gcc +-CXX= g++ +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-CXXFLAGS= $(CFLAGS) +-DFLAGS= -D_FILE_OFFSET_BITS=64 ++CC?= gcc ++CXX?= g++ ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CXXFLAGS?= $(CFLAGS) ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 + OBJS= + PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck + INCLUDES= -I.. +@@ -11,7 +11,7 @@ + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all:$(PROG) + +@@ -20,7 +20,7 @@ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -28,31 +28,31 @@ + lib: + + bamcheck:bamcheck.o +- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz + + bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h + $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c + + ace2sam:ace2sam.o +- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz + + md5sum-lite:md5sum-lite.o +- $(CC) $(CFLAGS) -o $@ md5sum-lite.o ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o + + md5sum-lite.o:md5.c md5.h + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz + + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c +--- samtools-0.1.20/misc/varfilter.py ++++ samtools-0.1.20/misc/varfilter.py +@@ -1,4 +1,4 @@ +-#!/software/bin/python ++#!/usr/bin/env python + + # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally + # diff --git a/sci-biology/samtools/files/samtools-1.5-buildsystem.patch b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch new file mode 100644 index 000000000000..c466e66a9d17 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.5-buildsystem.patch @@ -0,0 +1,413 @@ +--- a/config.mk.in ++++ b/config.mk.in +@@ -28,27 +28,26 @@ + # in the Makefile to reflect your configuration choices. If you don't run + # configure, the main Makefile contains suitable conservative defaults. + +-prefix = @prefix@ +-exec_prefix = @exec_prefix@ +-bindir = @bindir@ +-datarootdir = @datarootdir@ +-mandir = @mandir@ ++prefix = @prefix@ ++exec_prefix = @exec_prefix@ ++bindir = @bindir@ ++libdir = @libdir@ ++datarootdir = @datarootdir@ ++mandir = @mandir@ ++man1dir = $(mandir)/man1 + + CC = @CC@ ++AR = @AR@ + CPPFLAGS = @CPPFLAGS@ + CFLAGS = @CFLAGS@ + LDFLAGS = @LDFLAGS@ + LIBS = @LIBS@ + +-@Hsource@HTSDIR = @HTSDIR@ +-@Hsource@include $(HTSDIR)/htslib.mk +-@Hsource@include $(HTSDIR)/htslib_static.mk +-@Hsource@HTSLIB = $(HTSDIR)/libhts.a +-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS) +-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS) +-@Hsource@BGZIP = $(HTSDIR)/bgzip +-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@ +-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@ +-@Hinstall@HTSLIB_LIB = -lhts ++HTSLIB_CFLAGS = @HTSLIB_CFLAGS@ ++HTSLIB_LIBS = @HTSLIB_LIBS@ + +-CURSES_LIB = @CURSES_LIB@ ++NCURSES_CFLAGS = @NCURSES_CFLAGS@ ++NCURSES_LIBS = @NCURSES_LIBS@ ++ ++ZLIB_CFLAGS = @ZLIB_CFLAGS@ ++ZLIB_LIBS = @ZLIB_LIBS@ +--- a/configure.ac ++++ b/configure.ac +@@ -29,9 +29,6 @@ + AC_CONFIG_SRCDIR([bamtk.c]) + AC_CONFIG_HEADERS([config.h]) + +-m4_include([m4/ax_with_curses.m4]) +-m4_include([m4/ax_with_htslib.m4]) +- + dnl Copyright notice to be copied into the generated configure script + AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. + +@@ -39,73 +36,27 @@ + redistribute it. There is NO WARRANTY, to the extent permitted by law.]) + + AC_PROG_CC ++AM_PROG_AR + + AC_SYS_LARGEFILE + +-AX_WITH_HTSLIB +-if test "$ax_cv_htslib" != yes; then +- AC_MSG_ERROR([HTSlib development files not found +- +-Samtools uses HTSlib to parse bioinformatics file formats etc. Building it +-requires an unpacked HTSlib source tree (which will be built in conjunction +-with samtools) or a previously-installed HTSlib. In either case you may +-need to configure --with-htslib=DIR to locate the appropriate HTSlib. +- +-FAILED. You must supply an HTSlib in order to build samtools successfully.]) +-fi +- +-if test "$ax_cv_htslib_which" = source; then +- Hsource= +- Hinstall='#' +-else +- Hsource='#' +- Hinstall= +-fi +-AC_SUBST([Hsource]) +-AC_SUBST([Hinstall]) ++dnl htslib ++PKG_CHECK_MODULES([HTSLIB], [htslib]) + ++dnl ncurses + AC_ARG_WITH([curses], + [AS_HELP_STRING([--without-curses], + [omit curses support, so no curses library needed])]) + +-if test "$with_curses" != no; then +- AX_WITH_CURSES +- if test "$ax_cv_curses" != yes; then +- AC_MSG_ERROR([curses development files not found +- +-The 'samtools tview' command uses the curses text user interface library. +-Building samtools with tview requires curses/ncurses/etc development files +-to be installed on the build machine; you may need to ensure a package such +-as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based +-Linux distributions) is installed. +- +-FAILED. Either configure --without-curses or resolve this error to build +-samtools successfully.]) +- fi +-else +- CURSES_LIB= +- CURSES_CPPFLAGS= +- AC_SUBST([CURSES_LIB]) +- AC_SUBST([CURSES_CPPFLAGS]) +-fi +- +-save_LIBS=$LIBS +-zlib_devel=ok +-dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests +-AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;]) +-AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing]) +-LIBS=$save_LIBS +- +-if test $zlib_devel != ok; then +- AC_MSG_ERROR([zlib development files not found +- +-Samtools uses compression routines from the zlib library <http://zlib.net>. +-Building samtools requires zlib development files to be installed on the build +-machine; you may need to ensure a package such as zlib1g-dev (on Debian or +-Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed. ++AS_IF([test "x$with_curses" != "xno"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++ ++ AC_DEFINE([HAVE_CURSES], [1]) ++ AC_DEFINE([HAVE_NCURSES_H], [1]) ++]) + +-FAILED. This error must be resolved in order to build samtools successfully.]) +-fi ++dnl zlib ++PKG_CHECK_MODULES([ZLIB], [zlib]) + + AC_CONFIG_FILES([config.mk]) + AC_OUTPUT +--- a/Makefile ++++ b/Makefile +@@ -21,14 +21,6 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-CPPFLAGS = +-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LIBS = +- + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o + AOBJS= bam_index.o bam_plcmd.o sam_view.o \ +@@ -40,13 +32,6 @@ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ + bam_quickcheck.o bam_addrprg.o + +-prefix = /usr/local +-exec_prefix = $(prefix) +-bindir = $(exec_prefix)/bin +-datarootdir = $(prefix)/share +-mandir = $(datarootdir)/man +-man1dir = $(mandir)/man1 +- + # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) + misc_bindir = $(bindir) + +@@ -85,15 +70,14 @@ + + all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS) + +-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) +-ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) +-ALL_LIBS = -lz $(LIBS) ++ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS) ++ALL_LIBS = $(ZLIB_LIBS) $(LIBS) + + # Usually config.mk and config.h are generated by running configure + # or config.status, but if those aren't used create defaults here. + + config.mk: +- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@ ++ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@ + + config.h: + echo '/* Basic config.h generated by Makefile */' > $@ +@@ -133,17 +117,22 @@ + .c.o: + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $< ++ + + LIBST_OBJS = sam_opts.o sam_utils.o + + +-lib:libbam.a ++lib: libbam.so.1.0 + +-libbam.a:$(LOBJS) +- $(AR) -csru $@ $(LOBJS) ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) ++ ln -sf $@ libbam.so.1 ++ ln -sf $@ libbam.so + +-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread ++samtools: $(AOBJS) libbam.so.1.0 libst.a ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread + + # For building samtools and its test suite only: NOT to be installed. + libst.a: $(LIBST_OBJS) +@@ -151,58 +140,58 @@ + $(AR) -rcs $@ $(LIBST_OBJS) + + +-bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) +-bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h) +-bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) +-bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h) +-sam_h = sam.h $(htslib_sam_h) $(bam_h) +-sam_opts_h = sam_opts.h $(htslib_hts_h) +-sample_h = sample.h $(htslib_kstring_h) +- +-bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h +-bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) +-bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h) +-bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h) +-bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h) ++bam_h = bam.h ++bam2bcf_h = bam2bcf.h ++bam_lpileup_h = bam_lpileup.h ++bam_plbuf_h = bam_plbuf.h ++bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h) ++sam_h = sam.h $(bam_h) ++sam_opts_h = sam_opts.h ++sample_h = sample.h ++ ++bam.o: bam.c config.h $(bam_h) sam_header.h ++bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h) ++bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h) ++bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h) ++bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h) + bam_aux.o: bam_aux.c config.h $(bam_h) +-bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h ++bam_cat.o: bam_cat.c config.h samtools.h + bam_color.o: bam_color.c config.h $(bam_h) +-bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h) +-bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h +-bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h) +-bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h +-bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h +-bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) +-bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h) +-bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h +-bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h) +-bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h +-bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h +-bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h +-bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h +-bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h) ++bam_import.o: bam_import.c config.h $(bam_h) ++bam_index.o: bam_index.c config.h samtools.h ++bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) ++bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h ++bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h ++bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h) ++bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h) ++bam_quickcheck.o: bam_quickcheck.c config.h ++bam_reheader.o: bam_reheader.c config.h samtools.h ++bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h) ++bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h ++bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h ++bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h ++bam_stat.o: bam_stat.c config.h samtools.h ++bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h) + bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h) +-bam_flags.o: bam_flags.c config.h $(htslib_sam_h) +-bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h) +-bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h +-bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h) +-bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h) +-cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h) +-dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h) +-faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h +-padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h +-phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h) +-sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h) ++bam_flags.o: bam_flags.c config.h ++bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h) ++bamtk.o: bamtk.c config.h samtools.h version.h ++bedcov.o: bedcov.c config.h $(sam_opts_h) ++bedidx.o: bedidx.c config.h ++cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h) ++dict.o: dict.c config.h ++faidx.o: faidx.c config.h samtools.h ++padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h ++phase.o: phase.c config.h $(sam_opts_h) samtools.h ++sam.o: sam.c config.h $(sam_h) ++sam_header.o: sam_header.c config.h sam_header.h + sam_opts.o: sam_opts.c config.h $(sam_opts_h) + sam_utils.o: sam_utils.c config.h samtools.h +-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h) +-sample.o: sample.c config.h $(sample_h) $(htslib_khash_h) +-stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h) +-stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h) ++sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h) ++sample.o: sample.c config.h $(sample_h) ++stats_isize.o: stats_isize.c config.h stats_isize.h ++stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h) + + + # test programs +@@ -224,30 +213,30 @@ + + + test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + + test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread + +-test_test_h = test/test.h $(htslib_sam_h) ++test_test_h = test/test.h + + test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h) + test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o +@@ -256,34 +245,34 @@ + test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h) + test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h) + test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h) +-test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h) +-test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h) ++test/test.o: test/test.c config.h $(test_test_h) ++test/vcf-miniview.o: test/vcf-miniview.c config.h + + + # misc programs + + misc/ace2sam: misc/ace2sam.o +- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS) + + misc/maq2sam-short: misc/maq2sam-short.o +- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS) + + misc/maq2sam-long: misc/maq2sam-long.o +- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + + misc/md5fa: misc/md5fa.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS) + + misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) +- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS) + + misc/wgsim: misc/wgsim.o +- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS) + +-misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h) +-misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h) +-misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h) +-misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h) ++misc/ace2sam.o: misc/ace2sam.c config.h ++misc/md5fa.o: misc/md5fa.c config.h ++misc/md5sum-lite.o: misc/md5sum-lite.c config.h ++misc/wgsim.o: misc/wgsim.c config.h + + misc/maq2sam-short.o: misc/maq2sam.c config.h + $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml new file mode 100644 index 000000000000..fe27db1184af --- /dev/null +++ b/sci-biology/samtools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">samtools</remote-id> + <remote-id type="github">samtools/samtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/samtools/samtools-0.1.20-r3.ebuild b/sci-biology/samtools/samtools-0.1.20-r3.ebuild new file mode 100644 index 000000000000..5cfcfd7f6a79 --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.20-r3.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-single-r1 toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0.1-legacy" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + sys-libs/ncurses:0= + dev-lang/perl" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}/${P}-buildsystem.patch" +) + +src_prepare() { + default + # required, otherwise python_fix_shebang errors out + sed -i 's~/software/bin/python~/usr/bin/env python~' misc/varfilter.py || die + tc-export CC AR +} + +src_compile() { + local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" + emake dylib LIBCURSES="${_ncurses}" + emake LIBCURSES="${_ncurses}" +} + +src_install() { + # install executables and hide them away from sight + dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \ + misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck} + mv "${ED%/}"/usr/{bin,${PN}-${SLOT}} || die + mkdir "${ED%/}"/usr/bin || die + mv "${ED%/}"/usr/{${PN}-${SLOT},bin/} || die + + # ... do the same with the python script, but also fix the shebang + mv "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter{,-${SLOT}}.py || die + python_fix_shebang "${ED%/}"/usr/bin/${PN}-${SLOT}/varfilter-${SLOT}.py + + # fix perl shebangs + pushd "${ED%/}"/usr/bin/${PN}-${SLOT} >/dev/null || die + local i + for i in plot-bamcheck *.pl; do + sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die + done + popd >/dev/null || die + + dolib.so libbam-${SLOT}$(get_libname 1) + dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) + + insinto /usr/include/bam-${SLOT} + doins *.h + + mv ${PN}{,-${SLOT}}.1 || die + doman ${PN}-${SLOT}.1 + einstalldocs + + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi +} + +pkg_postinst() { + elog "This version of samtools should *not* be your first choice for working" + elog "with NGS data. It is installed solely for programs requiring it." + elog "It is recommended that you use >=sci-biology/samtools-1.2." +} diff --git a/sci-biology/samtools/samtools-1.5.ebuild b/sci-biology/samtools/samtools-1.5.ebuild new file mode 100644 index 000000000000..c2bc7ce89cf6 --- /dev/null +++ b/sci-biology/samtools/samtools-1.5.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools python-r1 toolchain-funcs + +DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-${PV}* + sys-libs/ncurses:0= + sys-libs/zlib + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}/${PN}-1.5-buildsystem.patch" ) + +src_prepare() { + default + + python_setup + python_fix_shebang misc/varfilter.py + + # remove bundled htslib + rm -r htslib-* || die + + eautoreconf +} + +src_test() { + local -x LD_LIBRARY_PATH="${S}" + default +} + +src_install() { + default + + # install libbam and headers + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest new file mode 100644 index 000000000000..cc814b318224 --- /dev/null +++ b/sci-biology/seaview/Manifest @@ -0,0 +1,9 @@ +DIST seaview_4.3.5.tar.gz 309530 SHA256 38050d6792eb799d61e5e849f76971a9c7d45f467e5c04fbc4363062d8e7100d SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a WHIRLPOOL 82fc7324bf1d934d69712629808d6b4178a5f2cdcf25351fb2fe2784f9cea0c1ec0aaaba7a3a08c84795108eb049394ceaab052af8cc0efbb0975064fa4e80e0 +DIST seaview_4.5.4.tar.gz 420608 SHA256 f4569ad7f1d8de2b141175b1122f036cb45f55f8e9e59e42d6026668e091e7ed SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301 WHIRLPOOL c52f7ac9d7d4c85d7670bdb3a87c9ba94904b25e11583ad8abf3de9f43fa3967d64b96d447ebb5ebe614053c4de64828d1c3c5763c64dc269e78fb3c49151886 +DIST seaview_4.6.tar.gz 424258 SHA256 6826a41bf2980922add66857abe42e3e6a19f0d1bb13845252745db7740c37bc SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6 WHIRLPOOL 50375ee836de8de50556a69054baa841f27025d679ce65953aee55d69c89129246eef8896b5833b5874cbdcbc55900dd4e37d4814c4f0a90097cb8c37f0ef1ae +EBUILD seaview-4.3.5.ebuild 2013 SHA256 a5e3ed9063835147e1227e4094941d7ffa34ba5ba44da9b4fd3b3e5aa55420ac SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945 WHIRLPOOL 26e9c72ac903782291e131da4d52059a4b1c79becacd431d00b0726272bc4e7f844626bede2fc7e36a28ccccfcb3a4b0e975d00c3c62d8dd45b39ba99542c597 +EBUILD seaview-4.5.4.ebuild 2013 SHA256 a5e3ed9063835147e1227e4094941d7ffa34ba5ba44da9b4fd3b3e5aa55420ac SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945 WHIRLPOOL 26e9c72ac903782291e131da4d52059a4b1c79becacd431d00b0726272bc4e7f844626bede2fc7e36a28ccccfcb3a4b0e975d00c3c62d8dd45b39ba99542c597 +EBUILD seaview-4.6.ebuild 1997 SHA256 6b57bec3393355d016145f9104ac66b33497cbe1787a9430e45b353739528c1b SHA512 5768df52c205ccfaa4d2d52ec753125dd77eb91a7b0be959dbc67aca00c0a66dc3f13b125d073450a81a06eea29880503981942042c77a0c6e1bb8f19f070cb8 WHIRLPOOL e666cc8ce9ee43e8ae7a9321d7eb5ecc557036aa464354c1a0b0d278d465968be73f77f7a2ea51e1b01eadf0f112973d07022c74ae60c5abcb09e75b1707c83f +MISC ChangeLog 3587 SHA256 4ed7e21c12bc6710319fe46602e6ee30c7436d79a6f5afe8273b754b35f74d5d SHA512 394452bc63381d8c47434cbbba52c40692b89157581a1c1466e5c7199e48d2e938e051ac1bc1d6819f0f2fd555868cc24ff0342c3d015d65548abbb37910891f WHIRLPOOL 4b68d6fa54617fb9308f52727bfa656e22d3550166b3b9a9ca4965a9a52d14368774d7bb9f4a8df43d0a34cc7c243d39b0f8a0efe8d99b05f1d4dcbd844277a0 +MISC ChangeLog-2015 8783 SHA256 0981ab2b9f7546a936e0e57ad0322f7007fc6a83e2b93f230acf665ac333d2bd SHA512 eb595983a51fc83a0d46ced9a6a5416ed2f61e7f1b33b8eeefbbb6979f486fba7582ce01a104ac28626d3ff17b7d4898613e09027f3d6f70bd42fb8e81b649f4 WHIRLPOOL 68f6eeda8f16a080a49467520b832a54341e9fbf265ac7e22d1e51f0f192edeecfc49e2716a860f2229577a194b90d2719756e6400e09b7ee68e91807a2fc19c +MISC metadata.xml 628 SHA256 1f936b9abe506aa04d855215dc6e7b0ea4a22abb2c464872b0f92dd6c2fe53ad SHA512 5ea98118394152f404bf39d35f3e5daf759e5a2107ea43141f7e8e54109ad0f41476e0cd820bcbde057bab96c4680be86cf8c25eacd4b6ec06122b633c062ad4 WHIRLPOOL d0c9e2cab8953fb461bf72802665030b15823cb3cf09611b8dab6f7d71d0c3b131f5f16e324f72310b61caf0484e3947eaf689aba5a58b322ac834e1a62dcac1 diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml new file mode 100644 index 000000000000..7e8eb04c0ab0 --- /dev/null +++ b/sci-biology/seaview/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + SeaView is a graphical multiple sequence alignment editor developped by + Manolo Gouy. SeaView is able to read and write various alignment + formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to + manually edit the alignment, and also to run DOT-PLOT or CLUSTALW + programs to locally improve the alignment. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/seaview/seaview-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild new file mode 100644 index 000000000000..33ee6f65ccbd --- /dev/null +++ b/sci-biology/seaview/seaview-4.3.5.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="A graphical multiple sequence alignment editor" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="+xft" + +CDEPEND=" + sys-libs/zlib + x11-libs/fltk:1 + x11-libs/libX11 + xft? ( + x11-libs/libXft + x11-libs/fltk:1[xft] )" +RDEPEND="${CDEPEND} + sci-biology/clustalw + || ( sci-libs/libmuscle sci-biology/muscle ) + sci-biology/phyml" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +src_prepare() { + # respect CXXFLAGS (package uses them as CFLAGS) + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "s:^CXX.*:CXX = $(tc-getCXX):" \ + -e "s:\$(OPT):${CXXFLAGS}:" \ + -e "s:^OPT:#OPT:" \ + -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ + -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ + -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ + -e "s:^USE_XFT:#USE_XFT:" \ + -e "s:^#HELPFILE:HELPFILE:" \ + -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ + -e "s:^#PHYMLNAME:PHYMLNAME:" \ + -e 's:-lXinerama::g' \ + -e 's:-lpng::g' \ + -e 's:-ljpeg::g' \ + -e 's:-lfontconfig::g' \ + -i Makefile || die "sed failed while editing Makefile" + + if use xft; then + sed \ + -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ + -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ + -i Makefile || die "sed failed while editing Makefile to enable xft" + else + sed -i -e "s:-lXft::" Makefile || die + fi +} + +src_install() { + dobin seaview + + # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile + insinto /usr/share/seaview + doins example.nxs seaview.html + + insinto /usr/share/seaview/images + doins seaview.xpm + + make_desktop_entry seaview Seaview + + doman seaview.1 +} diff --git a/sci-biology/seaview/seaview-4.5.4.ebuild b/sci-biology/seaview/seaview-4.5.4.ebuild new file mode 100644 index 000000000000..33ee6f65ccbd --- /dev/null +++ b/sci-biology/seaview/seaview-4.5.4.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="A graphical multiple sequence alignment editor" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="+xft" + +CDEPEND=" + sys-libs/zlib + x11-libs/fltk:1 + x11-libs/libX11 + xft? ( + x11-libs/libXft + x11-libs/fltk:1[xft] )" +RDEPEND="${CDEPEND} + sci-biology/clustalw + || ( sci-libs/libmuscle sci-biology/muscle ) + sci-biology/phyml" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +src_prepare() { + # respect CXXFLAGS (package uses them as CFLAGS) + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "s:^CXX.*:CXX = $(tc-getCXX):" \ + -e "s:\$(OPT):${CXXFLAGS}:" \ + -e "s:^OPT:#OPT:" \ + -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ + -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ + -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ + -e "s:^USE_XFT:#USE_XFT:" \ + -e "s:^#HELPFILE:HELPFILE:" \ + -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ + -e "s:^#PHYMLNAME:PHYMLNAME:" \ + -e 's:-lXinerama::g' \ + -e 's:-lpng::g' \ + -e 's:-ljpeg::g' \ + -e 's:-lfontconfig::g' \ + -i Makefile || die "sed failed while editing Makefile" + + if use xft; then + sed \ + -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ + -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ + -i Makefile || die "sed failed while editing Makefile to enable xft" + else + sed -i -e "s:-lXft::" Makefile || die + fi +} + +src_install() { + dobin seaview + + # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile + insinto /usr/share/seaview + doins example.nxs seaview.html + + insinto /usr/share/seaview/images + doins seaview.xpm + + make_desktop_entry seaview Seaview + + doman seaview.1 +} diff --git a/sci-biology/seaview/seaview-4.6.ebuild b/sci-biology/seaview/seaview-4.6.ebuild new file mode 100644 index 000000000000..4ad8ad61b72b --- /dev/null +++ b/sci-biology/seaview/seaview-4.6.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs + +DESCRIPTION="A graphical multiple sequence alignment editor" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+xft" + +RDEPEND=" + sys-libs/zlib + x11-libs/fltk:1 + x11-libs/libX11 + xft? ( + x11-libs/libXft + x11-libs/fltk:1[xft] ) + sci-biology/clustalw:2 + || ( sci-libs/libmuscle sci-biology/muscle ) + sci-biology/phyml" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +src_prepare() { + default + + # respect CXXFLAGS (package uses them as CFLAGS) + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "s:^CXX.*:CXX = $(tc-getCXX):" \ + -e "s:\$(OPT):${CXXFLAGS}:" \ + -e "s:^OPT:#OPT:" \ + -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ + -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ + -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ + -e "s:^USE_XFT:#USE_XFT:" \ + -e "s:^#HELPFILE:HELPFILE:" \ + -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ + -e "s:^#PHYMLNAME:PHYMLNAME:" \ + -e 's:-lXinerama::g' \ + -e 's:-lpng::g' \ + -e 's:-ljpeg::g' \ + -e 's:-lfontconfig::g' \ + -i Makefile || die "sed failed while editing Makefile" + + if use xft; then + sed \ + -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ + -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ + -i Makefile || die "sed failed while editing Makefile to enable xft" + else + sed -i -e "s:-lXft::" Makefile || die + fi +} + +src_install() { + dobin seaview + + # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile + insinto /usr/share/seaview + doins example.nxs seaview.html + + insinto /usr/share/seaview/images + doins seaview.xpm + + make_desktop_entry seaview Seaview + + doman seaview.1 +} diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest new file mode 100644 index 000000000000..d84c49f908c6 --- /dev/null +++ b/sci-biology/seqan/Manifest @@ -0,0 +1,11 @@ +AUX seqan-1.4.2-buildsystem.patch 870 SHA256 d824d014400b94778ea427c6e6220813201c41ded9a0ec0fbe1aeb891b69a626 SHA512 d769eb4137c8c0ddb7137ecfdb0673ba8648ae720673848cbb473a0c80d479b6e5c564c12f1a9dd01953d955605eb2f273e04808ae50058c565e997381c3f748 WHIRLPOOL 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93bc2a2b24ae8a84d45dcb2bfd3ad746913f0ab7d6883957e7ff3bff95994e2532ee9b08d59d186818ea86e21d9d39c203197bdcaeb306c340af1ec3ff533f81 WHIRLPOOL 10f701807471c698a5674cd1c4a04cc411b2551316a293b96affc9bc051278c6a46aaa0df34af60a79d89c2a1d161b54bb611de1433d1f44371887739859d7a6 +MISC ChangeLog-2015 1512 SHA256 68892efa58a06b8280c4f5695af5fa38a63f614fa321081efc2ae50ac132ce65 SHA512 e92d8bc043e9f7a9a1b4ae8ce81a07f228d2242425d346216a51f4086a7b9df1e6b7aabf2236f16ce665e36cbc9cc6913083b5a7e7db422052c3d44f1469710e WHIRLPOOL 26f302900373ff167adbe3ce18599acae05e3a2294701f02987d0e8016b01abbd6d3d5a138853ab5a762700b00a6d4b13aafdf1265e9e93051486a142bcd548d +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch new file mode 100644 index 000000000000..4c7893e90c05 --- /dev/null +++ b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch @@ -0,0 +1,30 @@ +Add default disabled flag to enable generation of documentation. +For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a +support library for legacy tools. + +--- seqan-1.4.2/CMakeLists.txt ++++ seqan-1.4.2/CMakeLists.txt +@@ -123,10 +123,12 @@ + add_subdirectory (core) + message (STATUS "Configuring extras") + add_subdirectory (extras) ++if (NOT SEQAN_NO_DOX) + message (STATUS "Configuring docs") + add_subdirectory (docs) + message (STATUS "Configuring manual") + add_subdirectory (manual) ++endif () + message (STATUS "Configuring sandbox") + add_subdirectory (sandbox) + message (STATUS "Configuring util/py_lib") +--- seqan-1.4.2/docs/main.py ++++ seqan-1.4.2/docs/main.py +@@ -123,7 +123,7 @@ + + # Done, print end message. + print 'Documentation created/updated.' +- return dddoc_html.WARNING_COUNT > 0 ++ return 0 + + + def main(argv): diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch new file mode 100644 index 000000000000..5baee4d8ebc0 --- /dev/null +++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch @@ -0,0 +1,16 @@ + core/include/seqan/index/index_qgram_openaddressing.h | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h +index 4a6c2e6..8cc9a42 100644 +--- a/core/include/seqan/index/index_qgram_openaddressing.h ++++ b/core/include/seqan/index/index_qgram_openaddressing.h +@@ -35,6 +35,8 @@ + #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H + #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H + ++#include <smmintrin.h> ++ + namespace SEQAN_NAMESPACE_MAIN + { + diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch new file mode 100644 index 000000000000..0f438ff07bce --- /dev/null +++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch @@ -0,0 +1,22 @@ + util/cmake/SeqAnBuildSystem.cmake | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake +index bcba2c0..d53cd01 100644 +--- a/util/cmake/SeqAnBuildSystem.cmake ++++ b/util/cmake/SeqAnBuildSystem.cmake +@@ -144,10 +144,10 @@ macro (seqan_register_apps) + set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1") + + # enable static linkage for seqan apps +- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) +- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") +- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") +- endif () ++# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) ++# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") ++# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") ++# endif () + + # Get all direct entries of the current source directory into ENTRIES. + file (GLOB ENTRIES diff --git a/sci-biology/seqan/files/seqan.pc.in b/sci-biology/seqan/files/seqan.pc.in new file mode 100644 index 000000000000..f917faef8ba3 --- /dev/null +++ b/sci-biology/seqan/files/seqan.pc.in @@ -0,0 +1,10 @@ +prefix=@CMAKE_INSTALL_PREFIX@ +exec_prefix=${prefix} +includedir=${prefix}/include + +Name: @CMAKE_PROJECT_NAME@ +Description: C++ library for biological sequence analysis +URL: http://www.seqan.de +Version: @SEQAN_VERSION_STRING@ +Requires: zlib +Cflags: -I${includedir} diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/seqan/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild new file mode 100644 index 000000000000..5fd8f1ae8a14 --- /dev/null +++ b/sci-biology/seqan/seqan-1.4.2-r1.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-any-r1 + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="http://www.seqan.de/" +SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" + +SLOT="$(get_version_component_range 1-2)" +LICENSE="BSD GPL-3" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse4_1 test" +REQUIRED_USE="cpu_flags_x86_sse4_1" + +RDEPEND=" + app-arch/bzip2 + sys-libs/zlib" +DEPEND=" + ${RDEPEND} + test? ( + $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') + ${PYTHON_DEPS} + )" + +PATCHES=( + "${FILESDIR}/${P}-shared.patch" + "${FILESDIR}/${P}-include.patch" + "${FILESDIR}/${P}-buildsystem.patch" +) + +pkg_setup() { + use test && python-any-r1_pkg_setup +} + +src_prepare() { + # pkg-config file, taken from seqan 2.1 + cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die + sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \ + -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \ + -e "s#@CMAKE_PROJECT_NAME@#${PN}#" \ + -e "s#@SEQAN_VERSION_STRING@#${PV}#" \ + -i ${PN}-${SLOT}.pc || die + + rm -f util/cmake/FindZLIB.cmake || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBoost_NO_BOOST_CMAKE=ON + -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY + -DSEQAN_NO_DOX=ON + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + + # SLOT header such that different seqan versions can be used in parallel + mkdir "${ED}"/usr/include/${PN}-${SLOT} || die + mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die + + # pkg-config file + insinto /usr/share/pkgconfig/ + doins ${PN}-${SLOT}.pc +} + +pkg_postinst() { + einfo "${CATEGORY}/${PF} is only intended as support library for older" + einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop" + einfo "any new software against the latest SeqAn release and not this one." +} diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild new file mode 100644 index 000000000000..2452ff0baea6 --- /dev/null +++ b/sci-biology/seqan/seqan-2.2.0-r1.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-any-r1 + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="http://www.seqan.de/" +SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse4_1 doc test" +REQUIRED_USE="cpu_flags_x86_sse4_1" + +RDEPEND=" + app-arch/bzip2 + sys-libs/zlib + !!sci-biology/seqan:2.0 + !!sci-biology/seqan:2.1 + !!sci-biology/seqan:2.2" +DEPEND=" + ${RDEPEND} + doc? ( + $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') + ${PYTHON_DEPS} + ) + test? ( + $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') + ${PYTHON_DEPS} + )" + +S="${WORKDIR}"/${PN}-${PN}-v${PV} + +pkg_setup() { + if use test || use doc; then + python-any-r1_pkg_setup + fi +} + +src_prepare() { + seqan_major_ver=$(get_version_component_range 1) + seqan_majorminor_ver=$(get_version_component_range 1-2) + + # install docs in proper Gentoo structure + sed -e "s#share/doc/seqan#share/doc/${PF}#" \ + -e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \ + -i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die + + # cmake module + sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \ + -e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \ + -e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${seqan_majorminor_ver})#" \ + -i util/cmake/FindSeqAn.cmake || die + + # pkg-config file + sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \ + -i util/pkgconfig/${PN}.pc.in || die + + rm -f util/cmake/FindZLIB.cmake || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY + -DSEQAN_NO_DOX=$(usex !doc) + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox +} + +src_install() { + cmake-utils_src_install + + # multi-version header such that different seqan versions can be installed in parallel + mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die + mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die + + # pkg-config file + mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die + + # create pkg-config symlink to restore default behaviour + dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc +} diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest new file mode 100644 index 000000000000..f23b17a02902 --- /dev/null +++ b/sci-biology/shrimp/Manifest @@ -0,0 +1,7 @@ +DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63 SHA512 1cb5d46d59102502acb26c33f1d5537644268704145f6e2ae7428aeaba6681cf1e63f7924d8ee696431675f2c4627da46fd0171f25bbb3296d247339c2d709eb WHIRLPOOL 0091c399830413a97b634d012b68015443ae04e4b3d6ffeb1665e3610226accfba9e21a2ed84935bb0bc4bca9dd92e122e96b905c96274255ad9b9527c1491fc +DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 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d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/shrimp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild new file mode 100644 index 000000000000..c71aa047c1a7 --- /dev/null +++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit flag-o-matic toolchain-funcs + +MY_PV=${PV//./_} + +DESCRIPTION="SHort Read Mapping Package" +HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" +SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" + +LICENSE="shrimp" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="custom-cflags" + +# file collision on /usr/bin/utils #453044 +DEPEND=" + !sci-biology/emboss + !sci-mathematics/cado-nfs" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/SHRiMP_${MY_PV} + +pkg_setup() { + if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then + elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" + die "C compiler lacks OPENMP support" + fi +} + +src_prepare() { + sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die + # respect LDFLAGS wrt 331823 + sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \ + -e 's/-static//' Makefile || die +} + +src_compile() { + append-flags -fopenmp + use custom-cflags || append-flags -O3 # per instructions in BUILDING + tc-export CXX + emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/README + dobin bin/* + insinto /usr/share/${PN} + doins -r utils + dodoc HISTORY README TODO SPLITTING_AND_MERGING +} diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild new file mode 100644 index 000000000000..2b57b032a1b2 --- /dev/null +++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit flag-o-matic python-single-r1 toolchain-funcs + +MY_PV=${PV//./_} + +DESCRIPTION="SHort Read Mapping Package" +HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" +SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" + +LICENSE="shrimp" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="custom-cflags +cpu_flags_x86_sse2" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +# file collision on /usr/bin/utils #453044 +DEPEND="!sci-mathematics/cado-nfs" +RDEPEND="${DEPEND} + ${PYTHON_DEPS}" + +S=${WORKDIR}/SHRiMP_${MY_PV} + +pkg_pretend() { + use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" +} + +pkg_setup() { + if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then + elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" + die "C compiler lacks OPENMP support" + fi + python-single-r1_pkg_setup +} + +src_prepare() { + sed \ + -e '1 a #include <stdint.h>' \ + -i common/dag_glue.cpp || die + # respect LDFLAGS wrt 331823 + sed \ + -e "s/LDFLAGS/LIBS/" \ + -e "s/\$(LD)/& \$(LDFLAGS)/" \ + -e 's/-static//' \ + -i Makefile || die + + append-flags -fopenmp + if ! use custom-cflags; then + append-flags -O3 + replace-flags -O* -O3 + fi + tc-export CXX + + cd utils || die + sed -e '/^#!/d' -i *py || die + sed -e '1i#!/usr/bin/python' -i *py || die +} + +src_compile() { + emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + local i + newdoc bin/README README.bin && rm bin/README + dobin bin/* utils/split-contigs utils/temp-sink + dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES + + pushd utils > /dev/null + + python_doscript *py + + rm *.py *.o *.c split-contigs temp-sink || die + insinto /usr/share/${PN} + doins -r * +} diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest new file mode 100644 index 000000000000..5245b963984d --- /dev/null +++ b/sci-biology/sibsim4/Manifest @@ -0,0 +1,5 @@ +DIST SIBsim4-0.20.tar.gz 32118 SHA256 ee02ae5f678d6843cf3ba267140dfccf9648a60d1f01263ae70d405723a35463 SHA512 3802520095e83d3c691804b661696095a4198c4b2a16385c55ccdc8e4e836f82cc9c2251a5d37cb5918c2ee80aeb81737d751e6b065fbfe9c64f1aee3e0ea0c8 WHIRLPOOL b6117192170a7c8b6bcc441c8b31b392410116d25045203ce33e5274a0a65608de408626df5a29fddbbbe34973869b055603defd58d06cbc6240925556b63282 +EBUILD sibsim4-0.20.ebuild 639 SHA256 395e41c62f5f6c5b37c030e277f208f515cf838257783e3cd57f51e4e8ce9a38 SHA512 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type="sourceforge">sibsim4</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild new file mode 100644 index 000000000000..bf431c666920 --- /dev/null +++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner" +HOMEPAGE="http://sibsim4.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/SIBsim4-${PV}" + +src_prepare() { + sed \ + -e 's/CFLAGS = /CFLAGS +=/' \ + -e '/^CC/s:=:?=:' \ + -e '/^OPT/d' \ + -e "s:-o:${LDFLAGS} -o:g" \ + -i "${S}/Makefile" || die + tc-export CC +} + +src_install() { + dobin SIBsim4 + doman SIBsim4.1 +} diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest new file mode 100644 index 000000000000..ff74c4d56e58 --- /dev/null +++ b/sci-biology/sim4/Manifest @@ -0,0 +1,6 @@ +AUX sim4-20030921-fix-build-system.patch 491 SHA256 f61c6bd531fa66de77e60a3eb0fcd1fbf0050900909be6b3b8e6f7e6ae06e327 SHA512 fdc737ccacd7cb4f7c5534af49587d7958f62dbe66a5197c38bda89af3cdd572231c10af75e8bb59120fa116f856f1ca5ba95279f9a2fe07228543588552f915 WHIRLPOOL 2b519969382729ce1aa2585a54bea390141e01c2df7b040b788e42b33ce5a4a97864ff0dd11b47f6786d217fece9a90928049f3eb2a55656ef6652d92e297cd9 +DIST sim4.tar.gz 60814 SHA256 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee SHA512 de7ee4094830262cb7ea8ed2f4573beed96df4b12f2915f669c52fd3fa40f5a4894cd94224e575bfb2588f9a6f19c0b73a38d6209d92a1dc644639a4927aa6b5 WHIRLPOOL b8d7cbcf44a03b5b13a51204e424e7e6ac2ab862e942c943b2a2f0d50bd1a823e3c1542fb2033f4b13f1539a636fb582c8d63b6406e2dc774f72f3eea7cc8004 +EBUILD sim4-20030921-r2.ebuild 553 SHA256 7eea5ed01863028a6640e75be0482c7efbe5e3b7bd39621715fc1a2e9865f997 SHA512 51fd5d759f62b005bc33b2fc37dbf8dc3f8b993d461d5dc2722ed93f8a8e51c19d21ea82105c3544ed23ad831c7e2d5c86e5c63aa3aa19937c4c354426e37f71 WHIRLPOOL 4267cbf1885b56d86cf96fd2bdedbb7f2ecd92c7eb8e3e03edbb15b87411b4d9f0197340d3426ab5dde6bbba84f679bfc9bf664fba6d7fc76eeef48b7e9e0241 +MISC ChangeLog 2485 SHA256 6270458054b23d23137856ecb7ebb2d48cb2f4f19de504de7399a4e42af6f85d SHA512 fd61ae1d8f5f27088860e8ff6c04e82de1b9beb08fa310882ff7839cbe7dad838d974f3f6a3875bd8a700cb6b4d3b7a9a375ba309777634503f614a4e948ac49 WHIRLPOOL d79ee3e790e820ddedc080e8649477620dae5b9263f76c1e1c105b11c2ec5603a724ecea6794e3b02d87d0dd5f696b1c8a57c222cc2f2fafd8402ab938c27d39 +MISC ChangeLog-2015 1401 SHA256 c43bba4aab69e4b6a96a907a221c706459b726c3e84460c91bfab41799995425 SHA512 ba70237e17cfdc2ca0553f0ebfd8f72d43ed5f28b5d8b89ea70a6e9d16155da0ff4e29e52519782fe635451fb266551afce9436c0d174a204d480faa8a5eccab WHIRLPOOL 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Sun's compilers under Solaris, ``-fast'' works well. + # For gcc, ``-O2'' works well. +-CC=cc +-CFLAGS=-O +-LDLIBS=-lm ++CC ?= gcc ++LDLIBS = -lm + + sim4: +- $(CC) -o sim4 -I. $(CFLAGS) *.c $(LDLIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o sim4 -I. *.c $(LDLIBS) + clean: + rm -f sim4 *.o diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml new file mode 100644 index 000000000000..6366d6fb797e --- /dev/null +++ b/sci-biology/sim4/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + sim4 is a similarity-based tool for aligning an expressed DNA sequence + (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects + end matches when the two input sequences overlap at one end (i.e., the + start of one sequence overlaps the end of the other).sim4 employs a + blast-based technique to first determine the basic matching blocks + representing the "exon cores". In this first stage, it detects all + possible exact matches of W-mers (i.e., DNA words of size W) between + the two sequences and extends them to maximal scoring gap-free + segments. In the second stage, the exon cores are extended into the + adjacent as-yet-unmatched fragments using greedy alignment algorithms, + and heuristics are used to favor configurations that conform to the + splice-site recognition signals (GT-AG, CT-AC). If necessary, the + process is repeated with less stringent parameters on the unmatched + fragments. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/sim4/sim4-20030921-r2.ebuild b/sci-biology/sim4/sim4-20030921-r2.ebuild new file mode 100644 index 000000000000..204ec82210ae --- /dev/null +++ b/sci-biology/sim4/sim4-20030921-r2.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="A program to align cDNA and genomic DNA" +HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html" +SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +S=${WORKDIR}/${PN}.2003-09-21 + +PATCHES=( "${FILESDIR}"/${PN}-20030921-fix-build-system.patch ) + +src_configure() { + tc-export CC +} + +src_install() { + dobin ${PN} + einstalldocs +} diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest new file mode 100644 index 000000000000..d90be00d3b92 --- /dev/null +++ b/sci-biology/snpfile/Manifest @@ -0,0 +1,9 @@ +AUX snpfile-2.0.1-ax-boost.patch 973 SHA256 a698df5bd1bfe04f40cdec8275fe3fecfced9c0e8cb43939e9b70cf3fd25cb5a SHA512 cb517e30c06620de9d007261d238325daf48709ccd875d90c0cc99049dfd0ce80a506a3e9a97c786ac8329b1f1463a810407927cf17c1a25689b03f413417b94 WHIRLPOOL e91815cd15321f0bbb62d9e73a9ea3ed80027b284a7a81d42c3c49c249f0dc6e8d23419f6606d0e51083fbf53f200168f60c26d6bf09a59d3bff7a34397783e3 +AUX snpfile-2.0.1-gcc44.patch 387 SHA256 349c6594759f16da2602415ff217c37bb677e2508437497b508c91ab4668956a SHA512 ac66850cae2bbbad9e1a989772490eb23ea3958c233e0fe32b20ffb3d7b5f547ff9d045974170c3302e8ca6bbbe5a2055acad24bb80cc6a3c527c3164e3f0e84 WHIRLPOOL f72f1321fce7941981780246d8837d260097eaf71ad1f352ae2f7407971a6625f2f9fc319904bb95ceba190d9e51b63212901798f8bcd31114e7724eee6adc00 +AUX snpfile-2.0.1-gentoo.diff 20224 SHA256 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f1f9fd9c8afbf372df12122953fceae78c14e2835843ad48587cb2aff073cd1bdad5bc70e2b9ca4a74d4f6e63ae6acaf92fff815d411c25fef56596b3841df2e WHIRLPOOL 07f7460167f61aabf397d418c194ad02f0e00f23240a4e28b39aa3aec01524a9664fb78d3c6e90f76b2def9cfe12a639fe9460dee115be34972c156d845b9b90 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch new file mode 100644 index 000000000000..f77b476f990d --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch @@ -0,0 +1,35 @@ +Modernise autoconf code to use modern archive macros. + +--- a/configure.in ++++ b/configure.in +@@ -1,7 +1,7 @@ + AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) + AM_INIT_AUTOMAKE + AC_CONFIG_MACRO_DIR([m4]) +-AM_CONFIG_HEADER(config.hh) ++AC_CONFIG_HEADERS([config.hh]) + + LT_INIT + AC_PROG_CXX +@@ -14,18 +14,9 @@ + fi + AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix]) + +-AX_BOOST([1.33.1],, +-AC_ERROR([[ +-************************************************************************ +-************************************************************************ +-The Boost library was not found on this system. We use this library +-extensively, and cannot proceed without it. You can obtain it from +-<http://www.boost.org>. +-************************************************************************ +-************************************************************************ +-]]) +-) +- ++AX_BOOST_BASE([1.33.1]) ++AX_BOOST_PROGRAM_OPTIONS ++AX_BOOST_SIGNALS + + AC_OUTPUT([ + Makefile diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch new file mode 100644 index 000000000000..2b79c2492ede --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch @@ -0,0 +1,12 @@ +diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh +--- snpfile-2.0.1.orig/input_archive.hh 2008-05-03 17:25:44.000000000 +0300 ++++ snpfile-2.0.1/input_archive.hh 2009-07-26 21:26:10.000000000 +0300 +@@ -26,6 +26,8 @@ + #ifndef INPUT_ARCHIVE_HH_INCLUDED + #define INPUT_ARCHIVE_HH_INCLUDED + ++#include <stdint.h> ++ + #include <string> + + #include "archive_common.hh" diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff new file mode 100644 index 000000000000..b2a8a6b630ce --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff @@ -0,0 +1,533 @@ +Fixing as-needed issues, provide shared libs + +https://bugs.gentoo.org/show_bug.cgi?id=294971 + +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,440 +1,92 @@ + ACLOCAL_AMFLAGS = -I m4 + +-AM_CXXFLAGS = +-AM_CXXFLAGS += -Wall +-AM_CXXFLAGS += $(BOOST_CPPFLAGS) ++AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS) ++SUFFIXES = .cc + +- +-# for testing +-AM_CXXFLAGS += -g -O2 #-lefence +- +-# for profiling +-#CXXFLAGS += -O3 -g -pg +-#AM_CXXFLAGS += -O3 -g -pg +- +-# for production +-#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG +-#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG +- +-# for coverage testing +-#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations +-#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations +- +- +-lib_LIBRARIES = libsnpfile.a ++lib_LTLIBRARIES = libsnpfile.la + + noinst_PROGRAMS = +-TESTS = +-EXTRA_DIST = +-bin_PROGRAMS = + + # conversion tools +-bin_PROGRAMS += text2snpfile +-bin_PROGRAMS += snpfile2text +-bin_PROGRAMS += snpfile2fastPHASE +-bin_PROGRAMS += fastPHASE2snpfile +-bin_PROGRAMS += snpfile2haploview +-bin_PROGRAMS += beagle_phase_snpfile ++bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \ ++ snpfile2haploview beagle_phase_snpfile + + # data extraction tools +-bin_PROGRAMS += snpfile_genotype_count +-bin_PROGRAMS += snpfile_phenotypes +-bin_PROGRAMS += snpfile_markers +- +-bin_PROGRAMS += snpfile_metadata_info +-bin_PROGRAMS += snpfile_set_metadata +-bin_PROGRAMS += snpfile_get_metadata ++bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers ++ ++bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata + + # other tools + noinst_PROGRAMS += snpfile_split_on_column + + # tests +-noinst_PROGRAMS += matrix_test +-TESTS += matrix_test +-noinst_PROGRAMS += file_test +-TESTS += file_test +-noinst_PROGRAMS += file_matrix_test +-TESTS += file_matrix_test +-noinst_PROGRAMS += readonly_matrix_test +-TESTS += readonly_matrix_test +-noinst_PROGRAMS += archives_test +-TESTS += archives_test +-noinst_PROGRAMS += metadata_access_test +-TESTS += metadata_access_test +-noinst_PROGRAMS += metadata_types_test +-TESTS += metadata_types_test +-noinst_PROGRAMS += iterators_test +-TESTS += iterators_test +-noinst_PROGRAMS += tabulate_test +-TESTS += tabulate_test +-noinst_PROGRAMS += metadata_filtering_test +-TESTS += metadata_filtering_test ++TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \ ++ metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test ++ ++noinst_PROGRAMS += $(TESTS) + + #Utils for testing across different machines +-noinst_PROGRAMS += make_test_snpfile +-noinst_PROGRAMS += test_test_snpfile ++noinst_PROGRAMS += make_test_snpfile test_test_snpfile + + # other experiments... +-noinst_PROGRAMS += row_metadata_experiment +-noinst_PROGRAMS += metadata_cache_prototype +-noinst_PROGRAMS += matrix_benchmark +-noinst_PROGRAMS += matrix_benchmark_write +-noinst_PROGRAMS += matrix_benchmark_read +- +- +- +-matrix_test_LDADD = +-matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_test_SOURCES = +-matrix_test_SOURCES += test_util.hh test_util.cc +-matrix_test_SOURCES += matrix.hh matrix.cc +-matrix_test_SOURCES += array_matrix.hh array_matrix.cc +-matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-matrix_test_SOURCES += input_archive.hh +-matrix_test_SOURCES += output_archive.hh +-matrix_test_SOURCES += metadata.hh metadata.cc +-matrix_test_SOURCES += snpfile.hh snpfile.cc +-matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_test_SOURCES += matrix_test.cc +- +- +-file_test_LDADD = +-file_test_LDADD += $(BOOST_SIGNALS_LIB) +-file_test_SOURCES = +-file_test_SOURCES += test_util.hh test_util.cc +-file_test_SOURCES += metadata.hh metadata.cc +-file_test_SOURCES += snpfile.hh snpfile.cc +-file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-file_test_SOURCES += file_test.cc +-file_test_SOURCES += metadata_access.hh +-file_test_SOURCES += input_archive.hh +-file_test_SOURCES += output_archive.hh +- +-file_matrix_test_LDADD = +-file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-file_matrix_test_SOURCES = +-file_matrix_test_SOURCES += test_util.hh test_util.cc +-file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-file_matrix_test_SOURCES += matrix.hh matrix.cc +-file_matrix_test_SOURCES += input_archive.hh +-file_matrix_test_SOURCES += output_archive.hh +-file_matrix_test_SOURCES += metadata.hh metadata.cc +-file_matrix_test_SOURCES += snpfile.hh snpfile.cc +-file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-file_matrix_test_SOURCES += file_matrix_test.cc +- +- +-readonly_matrix_test_LDADD = +-readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-readonly_matrix_test_SOURCES = +-readonly_matrix_test_SOURCES += test_util.hh test_util.cc +-readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc +-readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-readonly_matrix_test_SOURCES += matrix.hh matrix.cc +-readonly_matrix_test_SOURCES += input_archive.hh +-readonly_matrix_test_SOURCES += output_archive.hh +-readonly_matrix_test_SOURCES += metadata.hh metadata.cc +-readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc +-readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-readonly_matrix_test_SOURCES += readonly_matrix_test.cc +- +- +-archives_test_SOURCES = +-archives_test_SOURCES += input_archive.hh +-archives_test_SOURCES += output_archive.hh +-archives_test_SOURCES += archives_test.cc +- +- +-metadata_access_test_LDADD = +-metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_access_test_SOURCES = +-metadata_access_test_SOURCES += test_util.hh test_util.cc +-metadata_access_test_SOURCES += metadata.hh metadata.cc +-metadata_access_test_SOURCES += snpfile.hh snpfile.cc +-metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-metadata_access_test_SOURCES += input_archive.hh +-metadata_access_test_SOURCES += output_archive.hh +-metadata_access_test_SOURCES += serialization_trait.hh +-metadata_access_test_SOURCES += metadata_access_test.cc +- +- +-metadata_types_test_LDADD = +-metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_types_test_SOURCES = +-metadata_types_test_SOURCES += test_util.hh test_util.cc +-metadata_types_test_SOURCES += metadata.hh metadata.cc +-metadata_types_test_SOURCES += snpfile.hh snpfile.cc +-metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-metadata_types_test_SOURCES += input_archive.hh +-metadata_types_test_SOURCES += output_archive.hh +-metadata_types_test_SOURCES += serialization_trait.hh +-metadata_types_test_SOURCES += metadata_types_test.cc +- +- +-iterators_test_SOURCES = +-iterators_test_SOURCES += iterators.hh +-iterators_test_SOURCES += array_matrix.hh array_matrix.cc +-iterators_test_SOURCES += matrix.hh matrix.cc +-iterators_test_SOURCES += iterators_test.cc +- +- +-tabulate_test_SOURCES = +-tabulate_test_SOURCES += tabulate.hh +-tabulate_test_SOURCES += array_matrix.hh array_matrix.cc +-tabulate_test_SOURCES += matrix.hh matrix.cc +-tabulate_test_SOURCES += tabulate_test.cc +- +- +-metadata_filtering_test_SOURCES = +-metadata_filtering_test_SOURCES += matrix.hh matrix.cc +-metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc +-metadata_filtering_test_SOURCES += metadata_filtering.hh +-metadata_filtering_test_SOURCES += metadata_filtering_test.cc +- +- +-make_test_snpfile_LDADD = +-make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-make_test_snpfile_SOURCES = +-make_test_snpfile_SOURCES += metadata.hh metadata.cc +-make_test_snpfile_SOURCES += snpfile.hh snpfile.cc +-make_test_snpfile_SOURCES += matrix.hh matrix.cc +-make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc +-make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc +-make_test_snpfile_SOURCES += input_archive.hh +-make_test_snpfile_SOURCES += output_archive.hh +-make_test_snpfile_SOURCES += make_test_snpfile.cc +- +- +-test_test_snpfile_LDADD = +-test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-test_test_snpfile_SOURCES = +-test_test_snpfile_SOURCES += metadata.hh metadata.cc +-test_test_snpfile_SOURCES += snpfile.hh snpfile.cc +-test_test_snpfile_SOURCES += matrix.hh matrix.cc +-test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc +-test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc +-test_test_snpfile_SOURCES += input_archive.hh +-test_test_snpfile_SOURCES += output_archive.hh +-test_test_snpfile_SOURCES += test_test_snpfile.cc +- +- +-row_metadata_experiment_LDADD = +-row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB) +-row_metadata_experiment_SOURCES = +-row_metadata_experiment_SOURCES += matrix.hh matrix.cc +-row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc +-row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc +-row_metadata_experiment_SOURCES += input_archive.hh +-row_metadata_experiment_SOURCES += output_archive.hh +-row_metadata_experiment_SOURCES += metadata.hh metadata.cc +-row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc +-row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc +-row_metadata_experiment_SOURCES += test_util.hh test_util.cc +-row_metadata_experiment_SOURCES += row_metadata_experiment.cc +- +- +-metadata_cache_prototype_SOURCES = +-metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc +-metadata_cache_prototype_LDFLAGS = +-metadata_cache_prototype_LDFLAGS += -L. +-metadata_cache_prototype_LDADD = +-metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_cache_prototype_LDADD += -lsnpfile +- +- +-matrix_benchmark_LDADD = +-matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_SOURCES = +-matrix_benchmark_SOURCES += test_util.hh test_util.cc +-matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc +-matrix_benchmark_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_SOURCES += input_archive.hh +-matrix_benchmark_SOURCES += output_archive.hh +-matrix_benchmark_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_SOURCES += timing.hh timing.cc +-matrix_benchmark_SOURCES += matrix_benchmark.cc +- +- +-matrix_benchmark_write_LDADD = +-matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_write_SOURCES = +-matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_write_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_write_SOURCES += input_archive.hh +-matrix_benchmark_write_SOURCES += output_archive.hh +-matrix_benchmark_write_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_write_SOURCES += timing.hh timing.cc +-matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc +- +- +-matrix_benchmark_read_LDADD = +-matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_read_SOURCES = +-matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_read_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_read_SOURCES += input_archive.hh +-matrix_benchmark_read_SOURCES += output_archive.hh +-matrix_benchmark_read_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_read_SOURCES += timing.hh timing.cc +-matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc ++noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ ++ matrix_benchmark_write matrix_benchmark_read ++ ++LDADD = $(top_builddir)/libsnpfile.la ++ ++matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc ++ ++file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \ ++ output_archive.hh ++ ++file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ file_matrix_test.cc ++ ++readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ readonly_matrix_test.cc + ++archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc ++ ++metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ serialization_trait.hh metadata_access_test.cc ++ ++metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ serialization_trait.hh metadata_types_test.cc ++ ++iterators_test_SOURCES = iterators.hh iterators_test.cc ++ ++tabulate_test_SOURCES = tabulate.hh tabulate_test.cc ++ ++metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc ++ ++make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc ++ ++test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc ++ ++row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \ ++ row_metadata_experiment.cc ++ ++matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \ ++ output_archive.hh timing.hh timing.cc matrix_benchmark.cc ++ ++matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \ ++ timing.hh timing.cc matrix_benchmark_write.cc ++ ++matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \ ++ timing.hh timing.cc matrix_benchmark_read.cc ++ ++snpfile_genotype_count_SOURCES = genotype_count.cc + + snpfileincludedir = $(includedir)/snpfile +-snpfileinclude_HEADERS = +-snpfileinclude_HEADERS += common.hh +-snpfileinclude_HEADERS += matrix.hh +-snpfileinclude_HEADERS += file_matrix.hh +-snpfileinclude_HEADERS += array_matrix.hh +-snpfileinclude_HEADERS += byte_order_handler.hh +-snpfileinclude_HEADERS += metadata.hh +-snpfileinclude_HEADERS += metadata_access.hh +-snpfileinclude_HEADERS += archive_common.hh +-snpfileinclude_HEADERS += archives.hh +-snpfileinclude_HEADERS += input_archive.hh +-snpfileinclude_HEADERS += output_archive.hh +-snpfileinclude_HEADERS += snpfile.hh +-snpfileinclude_HEADERS += serialization_trait.hh +-snpfileinclude_HEADERS += type_trait.hh +-snpfileinclude_HEADERS += iterators.hh +-snpfileinclude_HEADERS += tabulate.hh +- +-libsnpfile_a_SOURCES = +-libsnpfile_a_SOURCES += common.hh +-libsnpfile_a_SOURCES += matrix.hh matrix.cc +-libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc +-libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh +-libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh +-libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh +-libsnpfile_a_SOURCES += archive_common.hh +-libsnpfile_a_SOURCES += archives.hh +-libsnpfile_a_SOURCES += input_archive.hh +-libsnpfile_a_SOURCES += output_archive.hh +-libsnpfile_a_SOURCES += snpfile.hh snpfile.cc +-libsnpfile_a_SOURCES += serialization_trait.hh +-libsnpfile_a_SOURCES += type_trait.hh +- +-text2snpfile_SOURCES = +-text2snpfile_SOURCES += text2snpfile.cc +-text2snpfile_LDFLAGS = +-text2snpfile_LDFLAGS += -L. +-text2snpfile_LDADD = +-text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-text2snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-text2snpfile_LDADD += -lsnpfile +- +-snpfile2text_SOURCES = +-snpfile2text_SOURCES += snpfile2text.cc +-snpfile2text_LDFLAGS = +-snpfile2text_LDFLAGS += -L. +-snpfile2text_LDADD = +-snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2text_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2text_LDADD += -lsnpfile +- +- +-snpfile2fastPHASE_SOURCES = +-snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc +-snpfile2fastPHASE_LDFLAGS = +-snpfile2fastPHASE_LDFLAGS += -L. +-snpfile2fastPHASE_LDADD = +-snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2fastPHASE_LDADD += -lsnpfile +- +-fastPHASE2snpfile_SOURCES = +-fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc +-fastPHASE2snpfile_LDFLAGS = +-fastPHASE2snpfile_LDFLAGS += -L. +-fastPHASE2snpfile_LDADD = +-fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-fastPHASE2snpfile_LDADD += -lsnpfile +- +- +-snpfile2haploview_SOURCES = +-snpfile2haploview_SOURCES += snpfile2haploview.cc +-snpfile2haploview_LDFLAGS = +-snpfile2haploview_LDFLAGS += -L. +-snpfile2haploview_LDADD = +-snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2haploview_LDADD += -lsnpfile +- +- +-beagle_phase_snpfile_SOURCES = +-beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc +-beagle_phase_snpfile_LDFLAGS = +-beagle_phase_snpfile_LDFLAGS += -L. +-beagle_phase_snpfile_LDADD = +-beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-beagle_phase_snpfile_LDADD += -lsnpfile +- +-snpfile_genotype_count_SOURCES = +-snpfile_genotype_count_SOURCES += genotype_count.cc +-snpfile_genotype_count_LDFLAGS = +-snpfile_genotype_count_LDFLAGS += -L. +-snpfile_genotype_count_LDADD = +-snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_genotype_count_LDADD += -lsnpfile +- +-snpfile_phenotypes_SOURCES = +-snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc +-snpfile_phenotypes_LDFLAGS = +-snpfile_phenotypes_LDFLAGS += -L. +-snpfile_phenotypes_LDADD = +-snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_phenotypes_LDADD += -lsnpfile +- +-snpfile_markers_SOURCES = +-snpfile_markers_SOURCES += snpfile_markers.cc +-snpfile_markers_LDFLAGS = +-snpfile_markers_LDFLAGS += -L. +-snpfile_markers_LDADD = +-snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_markers_LDADD += -lsnpfile +- +-snpfile_metadata_info_SOURCES = +-snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc +-snpfile_metadata_info_LDFLAGS = +-snpfile_metadata_info_LDFLAGS += -L. +-snpfile_metadata_info_LDADD = +-snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_metadata_info_LDADD += -lsnpfile +- +-snpfile_set_metadata_SOURCES = +-snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc +-snpfile_set_metadata_LDFLAGS = +-snpfile_set_metadata_LDFLAGS += -L. +-snpfile_set_metadata_LDADD = +-snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_set_metadata_LDADD += -lsnpfile +- +-snpfile_get_metadata_SOURCES = +-snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc +-snpfile_get_metadata_LDFLAGS = +-snpfile_get_metadata_LDFLAGS += -L. +-snpfile_get_metadata_LDADD = +-snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_get_metadata_LDADD += -lsnpfile +- +-snpfile_split_on_column_SOURCES = +-snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc +-snpfile_split_on_column_LDFLAGS = +-snpfile_split_on_column_LDFLAGS += -L. +-snpfile_split_on_column_LDADD = +-snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_split_on_column_LDADD += -lsnpfile ++snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \ ++ byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \ ++ archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \ ++ type_trait.hh iterators.hh tabulate.hh ++ ++libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \ ++ array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \ ++ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ ++ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ ++ type_trait.hh ++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) ++ +--- a/configure.in ++++ b/configure.in +@@ -1,10 +1,11 @@ + AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) + AM_INIT_AUTOMAKE ++AC_CONFIG_MACRO_DIR([m4]) + AM_CONFIG_HEADER(config.hh) + ++LT_INIT + AC_PROG_CXX + AC_PROG_INSTALL +-AC_PROG_RANLIB + + if test "x$prefix" != xNONE; then + thePREFIX=$prefix diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch new file mode 100644 index 000000000000..2211aa36c0ca --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch @@ -0,0 +1,23 @@ + Makefile.am | 4 ++-- + 1 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 06fd733..5805c48 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile + noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ + matrix_benchmark_write matrix_benchmark_read + +-LDADD = $(top_builddir)/libsnpfile.la ++LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ + + matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc + +@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix + metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ + input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ + type_trait.hh +-libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) ++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ + diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/snpfile/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild new file mode 100644 index 000000000000..bbeb3111901f --- /dev/null +++ b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="A library and API for manipulating large SNP datasets" +HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/" +SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-libs/boost:=" +DEPEND=" + ${RDEPEND} + >=sys-devel/autoconf-archive-2016.09.16" + +PATCHES=( + "${FILESDIR}"/${P}-gcc44.patch + "${FILESDIR}"/${P}-gentoo.diff + "${FILESDIR}"/${P}-gold.patch + "${FILESDIR}"/${P}-ax-boost.patch +) + +src_prepare() { + default + mv configure.{in,ac} || die + rm m4/ax_boost.m4 || die + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-biology/stride/Manifest b/sci-biology/stride/Manifest new file mode 100644 index 000000000000..56dab2b064db --- /dev/null +++ b/sci-biology/stride/Manifest @@ -0,0 +1,7 @@ +AUX stride-LDFLAGS.patch 280 SHA256 3b2387a0649d76a24d5e9ed611ec3da43ca7844a3ce3704ebbad63699328fd10 SHA512 d3fc5fec53066fc5f015a2b741bf5e3a236db4eee04ae7908912036c0be004e9827228b9153188f2304c91eb44e9d029996b4d86eee7baf0d109ae87776504f8 WHIRLPOOL 97e620a9e57d76ff74bb973bea2f0841db6480856aecaee0d3ecc0da7a7889862613bdaf8675227b3207b9f19a4c358127e66880ce733b170adc27f21fcdaf8e +DIST stride-20060723-update.patch.bz2 5621 SHA256 8d48627c294b4efba67acba10fba47b20c0a8d5f7e06c2775a2d7eaaa0aa7b81 SHA512 e06eb68b907615e12dc1a9981be157400e9ffed9391a906cb4eb3ef4067b7027c26cc600298053bfc5d2bbbebbbfefe0e6b18d0e4f6fef2172768e6f95498af1 WHIRLPOOL fbe19cd7da96a845a001f5fcfb6c0aed7b9c4c152b48ef9ab9df63b1d72c9a97e545c9a6e12c5c58823210dd48050392b0a9c0758c1d57c3677ac5092de863f9 +DIST stride.tar.gz 56441 SHA256 d272700bccd046199f6ea1faed31a2a2662a7d5f13b7663736a1818ac18c87b9 SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b WHIRLPOOL 843c789eda18da69a670a134f8a19103381ac86d611a3e1f0b47e17c3d171a195b8064d131ec3f81a561a65d8536d5f8a8c3a490776646b50ecb6aee36c46536 +EBUILD stride-20011129-r1.ebuild 917 SHA256 3996ef9e80e77f2606a79fbe2749d7959a0b09c3539a9d51466cc4f353f70362 SHA512 633e21ef055594d0fdefd0d852b68b1585bda766616ab53fb3c69ee88e73161fea34d2c5428bc1b51261c04f65d760beeb7217eba61177fa108c4c505d4f013b WHIRLPOOL 719df7ca621cd02887165a8d32f0f8cc934eb7aecf7f8f53fb61bd5cd03fc89190c5b5f218994aeac605340bab3caabf495688bfffcad766e604fe2a5d7484ab +MISC ChangeLog 2497 SHA256 34c34cfc582afb6ad1be0d3af7e444f4dbf7318d89a8ff131fc0a78f78c6177e SHA512 5689c4ccd28fcd165a1e6a482b2ab69fa24173dead46bb9cb1234ebce361dc171e55237212efb6755dad39ec437274fc038e5372a67432c736d1a6d74fbd554d WHIRLPOOL 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index 000000000000..1761b12129bd --- /dev/null +++ b/sci-biology/stride/files/stride-LDFLAGS.patch @@ -0,0 +1,11 @@ +--- Makefile 2009-10-27 21:18:45.000000000 +0100 ++++ Makefile.new 2009-10-27 21:19:00.000000000 +0100 +@@ -12,7 +12,7 @@ + + + stride : $(OBJECT) +- $(CC) $(OBJECT) $(FLAGS) $(BINDIR)/stride ++ $(CC) $(LDFLAGS) $(OBJECT) $(FLAGS) $(BINDIR)/stride + + $(OBJECT) : stride.h protot.h + diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/stride/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild new file mode 100644 index 000000000000..c76883b861e1 --- /dev/null +++ b/sci-biology/stride/stride-20011129-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Protein secondary structure assignment from atomic coordinates" +HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/" +SRC_URI=" + ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2" + +SLOT="0" +LICENSE="STRIDE" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="" + +S="${WORKDIR}" + +RESTRICT="mirror bindist" + +src_prepare() { + # this patch updates the source to the most recent + # version which was kindly provided by the author + epatch \ + "${DISTDIR}/${PN}-20060723-update.patch.bz2" \ + "${FILESDIR}"/${PN}-LDFLAGS.patch + + # fix makefile + sed -e "/^CC/s|gcc -g|$(tc-getCC) ${CFLAGS}|" -i Makefile || \ + die "Failed to fix Makefile" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest new file mode 100644 index 000000000000..297927345e87 --- /dev/null +++ b/sci-biology/t-coffee/Manifest @@ -0,0 +1,10 @@ +AUX t-coffee-11.00-mayhem.patch 1230 SHA256 591a68129f5f62a1e7bf03b219bf98c9e2b0534a9abb0b9657fe81288bc94f13 SHA512 b2c232f3e517c9c944c3d13a96b8383f8875e2e968ed16df25e37c6bfeee106cf82f9107187081753fbcaba6e27713fe5f4ca51d2f859ea7e8744f3b2b41f035 WHIRLPOOL 5d66e781920835c6b7e283a380fe166a38f6a9ed250f808634b491fd5f4634c2f3bce4f77396e94113b10af8fc290ab04daf9076d5ab9bf75d8352b178025281 +AUX t-coffee-11.00-set_proper_dir_permissions.patch 1203 SHA256 df138a69c325fbd0f1beb12adaa2a1fc33bf38174dea128f036c2fe42e2d339f SHA512 fb19aae00ccc0824bcb757d32ee921159e9ece9c0336b3d663e0140ccfca77bf3fcce0eeb304517e41dc1dd4c9469c345c0c35fe8e7fdf120c6fddba4a4e1524 WHIRLPOOL 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33c84555d372ac808c763161ba35fc0c04b1aaaf400fe08b0d182c7dcb1f1c8d4f4e247bd0b51b744e1debc0e4805402d2195ca7b83be59d5001bcac0a5dbc6f WHIRLPOOL 3563ebc92c047fa51a9d23426428fcb495291695c53a1b3ee8663ccf14c265cde43c6069128a069f3b10264946b0e794e0b823713cfd1367b3cc2ef1c6105640 diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch new file mode 100644 index 000000000000..cbfeeabc181b --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch @@ -0,0 +1,25 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 21 Dec 2015 21:30:36 +0100 +Bug-Debian: https://bugs.debian.org/716373 +Description: Fix Mayhem issue + The idea behind this patch is that if there is a problem to set the HOME + directories no additional processes can exist and so we should *really* + exit. Somehow the printf_exit() function does some logic which ends up + in an endless loop and thus forcing the exit will help here. + . + Unfortunately this does not solve the issue completely since inside the + Exit call a "Segmentation fault" happens - so some broken pointer handling + seems to happen somewhere before. + +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -4642,7 +4642,8 @@ char *get_home_4_tcoffee () + } + else + { +- printf_exit (EXIT_FAILURE, stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM); ++ fprintf(stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM); ++ exit(EXIT_FAILURE); + } + + diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch new file mode 100644 index 000000000000..a3f47cd9fce2 --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch @@ -0,0 +1,35 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 21 Dec 2015 21:30:36 +0100 +Bug-Debian: https://bugs.debian.org/751579 +Description: When creating subdirectories in $HOME do not + make these world writable but keep users umask + +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in) + int a, buf; + char *dir; + ++ static char *home = getenv ("HOME"); ++ static mode_t oldmask = umask(0); ++ int change_umask = 0; ++ if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1; + + dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char)); + sprintf ( dir, "%s", dir_in); +@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in) + + if (access(dir, F_OK)==-1) + { +- mode_t oldmask = umask(0); +- mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO); +- umask(oldmask); +- ++ if ( change_umask == 1 ) mkdir (dir, 0777-oldmask); ++ else { ++ mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO); ++ umask(oldmask); ++ } + if ( access (dir, F_OK)==-1) + { + myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM)); } diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch new file mode 100644 index 000000000000..5b15108b3bfa --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch @@ -0,0 +1,21 @@ + t_coffee_source/makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile +index 9e01ba0..026b714 100644 +--- a/t_coffee_source/makefile ++++ b/t_coffee_source/makefile +@@ -1,6 +1,6 @@ + + t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o +- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm + + all: t_coffee TMalign + +@@ -8,4 +8,4 @@ clean: + rm *.o + + TMalign: +- $(FCC) TMalign.f -o TMalign ++ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml new file mode 100644 index 000000000000..d0787617064b --- /dev/null +++ b/sci-biology/t-coffee/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + T-Coffee is a multiple sequence alignment package. Given a set of + sequences (Proteins or DNA), T-Coffee generates a multiple sequence + alignment. Version 2.00 and higher can mix sequences and structures. + T-Coffee allows the combination of a collection of multiple/pairwise, + global or local alignments into a single model. It also allows to + estimate the level of consistency of each position within the new + alignment with the rest of the alignments. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild new file mode 100644 index 000000000000..919287c790f8 --- /dev/null +++ b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +MY_HASH="8cbe486" +MY_PV="${PV}.${MY_HASH}" +MY_P="T-COFFEE_distribution_Version_${MY_PV}" + +DESCRIPTION="A multiple sequence alignment package" +HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" +SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-biology/clustalw + sci-chemistry/tm-align" +DEPEND="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed \ + -e '/@/s:.*;:\t:g' \ + -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ + -i t_coffee_source/makefile || die + epatch \ + "${FILESDIR}"/${P}-mayhem.patch \ + "${FILESDIR}"/${P}-set_proper_dir_permissions.patch +} + +src_compile() { + [[ $(gcc-version) == "3.4" ]] || \ + [[ $(gcc-version) == "4.1" ]] && \ + append-flags -fno-unit-at-a-time + emake \ + V=1 \ + CC="$(tc-getCXX)" \ + CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \ + -C t_coffee_source t_coffee +} + +src_install() { + dobin t_coffee_source/t_coffee + + if use examples; then + insinto /usr/share/${PN} + doins -r example + fi +} diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild new file mode 100644 index 000000000000..9f32c135fb78 --- /dev/null +++ b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 toolchain-funcs versionator + +MY_PV="$(replace_version_separator 2 .r)" +MY_P="T-COFFEE_distribution_Version_${MY_PV}" + +DESCRIPTION="A multiple sequence alignment package" +HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" +SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-biology/clustalw + sci-chemistry/tm-align" +DEPEND="" + +S="${WORKDIR}/${MY_P}" + +die_compile() { + echo + eerror "If you experience an internal compiler error (consult the above" + eerror "messages), try compiling t-coffee using very modest compiler flags." + eerror "See bug #114745 on the Gentoo Bugzilla for more details." + die "Compilation failed" +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-flags.patch +} + +src_compile() { + [[ $(gcc-version) == "3.4" ]] || \ + [[ $(gcc-version) == "4.1" ]] && \ + append-flags -fno-unit-at-a-time + emake \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + -C t_coffee_source t_coffee +} + +src_install() { + dobin t_coffee_source/t_coffee + + if use examples; then + insinto /usr/share/${PN} + doins -r example + fi +} diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest new file mode 100644 index 000000000000..0c7873ed7863 --- /dev/null +++ b/sci-biology/tophat/Manifest @@ -0,0 +1,8 @@ +AUX tophat-2.1.1-fix-c++14.patch 655 SHA256 77bdb0077062ac54d3400d4b8e8cd64a402ce8e502f5186515a30a230c4f6bf0 SHA512 66f46da853ee56821c50d46cb6853f082009dfc4d5237ec82371db9e9f5435a5a84420e03955aec7ae80076d3da492e0be7ae7d34bced06ee2ea845ad23974ca WHIRLPOOL 7fdef9f723f816829059483f5804a1bdd197fe54d0e843dd47dc21e951be757db2c5197d99942ee437393cd5212cab0526ff512b2326b1e8e34e7091282b6936 +AUX tophat-2.1.1-python2-shebangs.patch 758 SHA256 c040207f777c7ae0ab21776ac6a590dd7adf1936b7b29ccac10e0e315400d31c SHA512 887e5a8b02c2e43a7fa35c9f98670dd722527c45454ca24d5e2f9d2f372267905d7e0142317769b14830706cf82868cb83ede970ffe527f736d71df794fd6342 WHIRLPOOL 4323ff6beba00aae98904388bd8983bc23f93d2edd6a8a0f35518d9dfaac22dff304893636362b49084bc73e8c0789418ab5da1930e3fe4f9416b97248f78bda +AUX tophat-2.1.1-unbundle-seqan-samtools.patch 5224 SHA256 6ea748a1185c485a2c257cb70103fe91b9c4133fc87af5b429beb97f34c4624c SHA512 d920cee92a0a694a34d6ac5b949e5b883bf9dcff338f36e227cb014732231b96461c02e75418972c85880169751a96c2367f6a4be6ce8c91f310b4b4f6858248 WHIRLPOOL d39046119c21d7d14b93e68800eb2f6780c9e8d853691ab634bcb37a8cdbc28c370d2c7d75231fab0fc9cf1758ac4b26ca4fd6085afa2afdb492cec68b71b349 +DIST tophat-2.1.1.tar.gz 2259554 SHA256 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc WHIRLPOOL 1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c +EBUILD tophat-2.1.1-r4.ebuild 2182 SHA256 aeb2961cda7f0137cb433f546f81a5c525fb6609980b42bc8e93ad2d0356b4f5 SHA512 b97690d43bc89aaafe2df3091602e3509cc1ef4ed2323a58aeb734329f587872325bf73ad69b899d467591bb7be5f685ebeb87376e5fab4b867831b3858c92f0 WHIRLPOOL 9a37fcfdf7574dce58eb9ddc1842a94c95066fe212ebee3d20aaa13608feb8b1c2a47cdff2dce483baefcb9f9d22461b97e856c30d08a386f46785e87650d034 +MISC ChangeLog 5031 SHA256 b2d1b226a5a334ca097fbe4f85a763499f81e61772ac37994729e792188a38ae SHA512 b2b79ab44987b781cd1a8e0dd4e1e94970666bcdf28902b146f8aa1ddfd808beab132623042ad5079b5f2b40a712d8be7afcc7de181a230b7f9dcec366c11ff4 WHIRLPOOL 2be3cc2ff83f1e342a20b92342ecbd6875437faa4ae112a394d34b22886be1b453539ee0b03afe7e44edfcc5f298dd461e19437b0431d6a3ee37dd919113d338 +MISC ChangeLog-2015 2307 SHA256 66a4e11a7ed49f16ba25f9cedd4fbc273a6a246eb154150276d5b64a642aa9cb SHA512 ed08c5028eb9569860aea71787a5e8d44d9d9d2995f593724371597162e6bec006a4a6d5a7d157facc1f1f6d0003c239ac2de05d1d96ffc58d345e5dfe4b9969 WHIRLPOOL 36e0146907a219cd618af78d36be2f3f60bec0eb187f4ef74f1881f40e049be306a4486fed747a8e78cba0c8d67173ae0175e3d47380abd180467a7c4fb0c4da +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch new file mode 100644 index 000000000000..e8168bb91438 --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch @@ -0,0 +1,14 @@ +Fix building with C++14, which errors out due to broken perfect forwarding signature. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594544 + +--- a/src/tophat_reports.cpp ++++ b/src/tophat_reports.cpp +@@ -2705,7 +2705,7 @@ + junction_stat.gtf_match = true; + junction_stat.accepted = true; + +- gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); ++ gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); + } + } + fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str()); diff --git a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch new file mode 100644 index 000000000000..5c38bcc072ef --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch @@ -0,0 +1,42 @@ +Make Python 2 explicit in python scripts + +--- a/src/bed_to_juncs ++++ b/src/bed_to_juncs +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + # encoding: utf-8 + """ + bed_to_juncs.py +--- a/src/contig_to_chr_coords ++++ b/src/contig_to_chr_coords +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + # encoding: utf-8 + """ + contig_to_chr_coords.py +--- a/src/sra_to_solid ++++ b/src/sra_to_solid +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + + """ + sra_to_solid.py +--- a/src/tophat-fusion-post ++++ b/src/tophat-fusion-post +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + + + """ +--- a/src/tophat.py ++++ b/src/tophat.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python2 + + # encoding: utf-8 + """ diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch new file mode 100644 index 000000000000..9d0a2694051a --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch @@ -0,0 +1,162 @@ +Unbundle the included samtools and SeqAn, and use system libraries. +See also: https://bugs.gentoo.org/show_bug.cgi?id=566494 + +Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend +on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594810 + +--- a/configure.ac ++++ b/configure.ac +@@ -28,26 +28,15 @@ + AC_PROG_INSTALL + AM_PATH_PYTHON([2.4]) + +-m4_include([ax_boost_base.m4]) +-m4_include([ax_boost_thread.m4]) + # CXXFLAGS="$CXXFLAGS $threadLib" + AX_BOOST_BASE([1.38.0]) ++AX_BOOST_SYSTEM + AX_BOOST_THREAD +-if test -z "$BOOST_THREAD_LIBS"; then ++if test -z "$BOOST_THREAD_LIB"; then + AC_MSG_ERROR([boost.thread not found. Aborting.]) + fi + + +-# BAM related: +- ac_bam_path=samtools-0.1.18 +- BAM_LIB="-lbam" +- BAM_LDFLAGS="-L./$ac_bam_path" +- BAM_CPPFLAGS="-I./$ac_bam_path" +- AC_SUBST(BAM_CPPFLAGS) +- AC_SUBST(BAM_LDFLAGS) +- AC_SUBST(BAM_LIB) +- +- + # Checks for header files. + AC_CHECK_HEADERS([stdlib.h string.h unistd.h]) + +@@ -80,32 +69,23 @@ + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" + +-AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], +- [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) +- + AC_ARG_ENABLE([debug], + [AS_HELP_STRING([--enable-debug], + [enable debugging info (default is no)])], + [], [enable_debug=no]) +-AC_ARG_ENABLE([optim], +- [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@], +- [set optimization level (default is 3)])], +- [if test "x$enable_optim" = xyes; then enable_optim=3; fi], +- [enable_optim=3]) + +-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) + AS_IF([test "x$enable_debug" = xyes], + [debug_CFLAGS="-DDEBUG"], + [debug_CFLAGS="-DNDEBUG"]) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" + CXXFLAGS="$CFLAGS" +-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" ++CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS" + LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" + + AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) +@@ -122,7 +102,7 @@ + -- ${PACKAGE_STRING} Configuration Results -- + C++ compiler: ${CXX} ${CXXFLAGS} + Linker flags: ${LDFLAGS} +- BOOST libraries: ${BOOST_THREAD_LIBS}" ++ BOOST libraries: ${BOOST_THREAD_LIB}" + + if test x"${GCC}" = x"yes" ; then + gcc_version=`${CC} --version | head -n 1` +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -683,17 +683,12 @@ + SeqAn-1.4.2/seqan/system/system_thread.h \ + SeqAn-1.4.2/seqan/version.h + +-SAMDIR = ./samtools-0.1.18 +-SAMLIB = libbam.a +-SAMPROG = samtools_0.1.18 +-BAM_LIB = -lbam +-BAM_CPPFLAGS = -I$(SAMDIR) +-BAM_LDFLAGS = -L$(SAMDIR) ++BAM_LIB = -lbam-0.1-legacy ++AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/ + + #-- progs to be installed in $prefix/bin + + bin_PROGRAMS = \ +- $(SAMPROG) \ + prep_reads \ + gtf_to_fasta \ + fix_map_ordering \ +@@ -722,9 +717,6 @@ + tophat2 \ + tophat + +-clean-local: +- cd $(SAMDIR) && make clean +- + tophat2: tophat2.sh + cp tophat2.sh tophat2 && chmod 755 tophat2 + +@@ -732,7 +724,7 @@ + sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat + + #-- tophat library for linking convienence +-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a ++noinst_LIBRARIES = libgc.a libtophat.a + + noinst_HEADERS = \ + reads.h \ +@@ -801,11 +793,11 @@ + prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +@@ -817,7 +809,7 @@ + juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) + tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp +@@ -844,15 +836,5 @@ + gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) + gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) + +- +-libbam_a_SOURCES = +-samtools_0_1_18_SOURCES = +- +-$(SAMPROG): $(SAMLIB) +- +- +-$(SAMLIB): +- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) .. +- + install-data-hook: + cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir) diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/tophat/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/tophat/tophat-2.1.1-r4.ebuild b/sci-biology/tophat/tophat-2.1.1-r4.ebuild new file mode 100644 index 000000000000..590f6eb2d20f --- /dev/null +++ b/sci-biology/tophat/tophat-2.1.1-r4.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools flag-o-matic python-single-r1 toolchain-funcs + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2" +HOMEPAGE="https://ccb.jhu.edu/software/tophat/" +SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-libs/boost:=[threads] + dev-python/intervaltree[${PYTHON_USEDEP}] + dev-python/sortedcontainers[${PYTHON_USEDEP}] + sci-biology/samtools:0.1-legacy + sci-biology/bowtie:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + sci-biology/seqan:1.4 + >=sys-devel/autoconf-archive-2016.09.16" + +PATCHES=( + "${FILESDIR}"/${P}-unbundle-seqan-samtools.patch + "${FILESDIR}"/${P}-fix-c++14.patch + "${FILESDIR}"/${P}-python2-shebangs.patch +) + +src_prepare() { + default + + # remove bundled libs + rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die + + sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \ + -i src/tophat.py src/common.cpp || die + + sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \ + -e '/^samtools-0\.1\.18\//d' \ + -e '/^SeqAn-1\.4\.2\//d' \ + -e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \ + -e 's:\$(top_builddir)\/src\/::' \ + -i src/Makefile.am || die + sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die + + # innocuous non-security flags, prevent log pollution + append-cflags -Wno-unused-but-set-variable -Wno-unused-variable + append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)" + + # remove ancient autoconf archive macros, wreaking havoc, + # depend on sys-devel/autoconf-archive instead, bug #594810 + rm {ax_boost_thread,ax_boost_base}.m4 || die + + eautoreconf +} + +src_configure() { + econf $(use_enable debug) +} + +src_install() { + default + + # delete bundled python modules + local i + for i in intervaltree sortedcontainers; do + rm -r "${ED%/}"/usr/bin/${i} || die + done +} + +pkg_postinst() { + optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1 +} diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest new file mode 100644 index 000000000000..4e3f2a1a7606 --- /dev/null +++ b/sci-biology/transfac/Manifest @@ -0,0 +1,5 @@ +DIST transfac32.tar.Z 3346266 SHA256 cf5c64e6f23037d73562d66f9dde56a767a8f31974a1c0906ec68edea3731a7f SHA512 d7004f90e57fa2b8839714e50b9ce1f67357db404adc1a5caddd1e9b86c8e3e9f4e85bbda15c4d6afed85da82ae8615f63260f9a3df9cfd79897d38896893b9f WHIRLPOOL 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type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + TRANSFAC® is a database of eukaryotic transcription factors, of their + genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is an old + public version available at the European Bioinformatics Institute. + TRANSFAC® is currently maintained by the BIOBASE company. Altough they + offer public access to a more recent version of the database, they + offer no free downloadable version. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/transfac/transfac-3.2-r1.ebuild b/sci-biology/transfac/transfac-3.2-r1.ebuild new file mode 100644 index 000000000000..91b16f4b4fe4 --- /dev/null +++ b/sci-biology/transfac/transfac-3.2-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="A database of eucaryotic transcription factors" +HOMEPAGE="http://www.gene-regulation.com/pub/databases.html" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z" + +LICENSE="public-domain" +SLOT="3" +# Minimal build keeps only the indexed files (if applicable) and the documentation. +# The non-indexed database is not installed. +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emboss minimal" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +S=${WORKDIR} + +src_compile() { + if use emboss; then + einfo + einfo "Indexing TRANSFAC for usage with EMBOSS" + EMBOSS_DATA="." tfextract -auto -infile class.dat || die "Indexing TRANSFAC failed" + einfo + fi +} + +src_install() { + newdoc readme.txt README + + if ! use minimal; then + insinto /usr/share/${PN}-${SLOT} + doins *.dat + fi + + if use emboss; then + insinto /usr/share/EMBOSS/data + doins tf* + fi +} diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest new file mode 100644 index 000000000000..33758246557c --- /dev/null +++ b/sci-biology/tree-puzzle/Manifest @@ -0,0 +1,6 @@ +AUX tree-puzzle-impl-dec.patch 380 SHA256 0d0941cb6030e089e224a2390a28193ec848c4b2aabf021888292e41df1a1f50 SHA512 092743fff8a305a41ef55afde3e058c1892d9c608bd05cb87de38a451c2b9cafc7749825347d5c245f1c6b1e84cf9d28b63bd4e7389440da5604766412290110 WHIRLPOOL d12a213adb3aefff795814859c02d9e8ed925b37bae31ad95d39344c6bc6514c05a3d03ef080ac9b8e7aff33f3a55d637c79c8df754c3ba6105e430b88b58282 +DIST tree-puzzle-5.2.tar.gz 875142 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751 WHIRLPOOL 145afdfc266809638d7b049beb65cdfc8fb6c108ecba831ba36fae938d58edd141fdf1762d9ce86269f0098043e7314b0ddefaa5e7f9b11cc6fd56a480b54d61 +EBUILD tree-puzzle-5.2.ebuild 1355 SHA256 ce039a7b96e3715546fee972f598d1836bcd132ef417fd59e73e7d3071cb7527 SHA512 44c268b736aa1769c4b85170094d620bdd12798e8d194d4d991f5a2078641d29a19216bb733636052337b93863dec386b0cf2bc3544401059c566205d6d5fe7d WHIRLPOOL 9ff0e12d871e78efd79f2744d3ca3a16f564de758ddcf5e265439ed70cb9c868f65503c43a9a0f0668fe4baf91b5ddf9b5904db955d7a088f018e3e41688e98c +MISC ChangeLog 2473 SHA256 51b8e8509bc9e744a8f35bdd17615cce04f51e49757600adf2bd5ca0bbb16c8d SHA512 467af996c4275a463e6dd2bf035ff537973704bed42f7cbf27e8dcbe358431b9cba5e3761c67da55b27280e91abc48f5452d5c5876a7f90b56a8bc6f11a2bf32 WHIRLPOOL ad40efb66a62171b0be1f3f8415f587a7a99c1cf68ac08a190b84adf4e5266a381d680da21c25cf7371931597ab4e1fb01261945f6c1c41f2bd2ed734d5b4b55 +MISC ChangeLog-2015 3415 SHA256 73662fc7bcbd74f8b2da79455934d8b6b40267e0b403c92d33866f6ceb156bfe SHA512 f9547f4a6f63a55aa98c0703d269a222a4cea38b4c7ac32dfc9965467b14f4e0be0fd0e502cb33b003cd6099c44dfed1c1ab5a49f2bf31a1777890d644d6a0a3 WHIRLPOOL 76a2553e06efafdf9864d87a2a774b05d48b3d13f2ad50bbcc20cc1f4cc54f841e5c3c1af97f43b6d9e4a76c60f1852ec71604cb73379f99ba1b70db3b20bf6d +MISC metadata.xml 1555 SHA256 d67ff8bb601bd9dd1950082180043e1e7991b177d1cebca4798484a401377fca SHA512 d74b3243cb62071c16a1728cb14e4c226644b8116dc032ac2d74a928260a252334583d1867ec3663533f36fa1bb746270f1d33f6fb4bae220af86eba668307b8 WHIRLPOOL 44a04284aa8e3216f620fe8efa6c327fb1fc689d15ce2be88639db23d98dae76c8f14854c1b1eccb34430c83f49181fa2ac735ae840e8b3e809f77cc016eac0c diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch new file mode 100644 index 000000000000..93b960f5c2b4 --- /dev/null +++ b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch @@ -0,0 +1,14 @@ + src/sprng/primes-lcg64.c | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c +index 8e5a7c9..fb04373 100644 +--- a/src/sprng/primes-lcg64.c ++++ b/src/sprng/primes-lcg64.c +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <string.h> + #include "primes-lcg64.h" + #include "primelist-lcg64.h" + diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml new file mode 100644 index 000000000000..4a34df848e3a --- /dev/null +++ b/sci-biology/tree-puzzle/metadata.xml @@ -0,0 +1,28 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + TREE-PUZZLE is a computer program to reconstruct phylogenetic trees + from molecular sequence data by maximum likelihood. It implements a + fast tree search algorithm, quartet puzzling, that allows analysis of + large data sets and automatically assigns estimations of support to + each internal branch. TREE-PUZZLE also computes pairwise maximum + likelihood distances as well as branch lengths for user specified + trees. Branch lengths can be calculated under the clock-assumption. In + addition, TREE-PUZZLE offers a novel method, likelihood mapping, to + investigate the support of a hypothesized internal branch without + computing an overall tree and to visualize the phylogenetic content of + a sequence alignment. TREE-PUZZLE also conducts a number of statistical + tests on the data set (chi-square test for homogeneity of base + composition, likelihood ratio clock test, Kishino-Hasegawa test). The + models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for + nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, + and F81 for two-state data. Rate heterogeneity is modeled by a discrete + Gamma distribution and by allowing invariable sites. The corresponding + parameters can be inferred from the data set. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild new file mode 100644 index 000000000000..27dd0bc2212f --- /dev/null +++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data" +HOMEPAGE="http://www.tree-puzzle.de" +SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="mpi" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +RESTRICT="test" + +pkg_setup () { + use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc. + Either disable the \"mpi\" USE flag to compile only the non-parallelized + version of the program, or use gcc as your compiler (CC=\"gcc\")." +} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-impl-dec.patch +} + +src_configure() { + default + + if ! use mpi; then + sed \ + -e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \ + -e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \ + -i "${S}"/src/Makefile || die + fi +} + +src_install() { + dobin src/puzzle + use mpi && dobin src/ppuzzle + dodoc AUTHORS ChangeLog README + + # User manual + insinto /usr/share/doc/${PF} + doins doc/tree-puzzle.pdf + + # Example data files + insinto /usr/share/${PN}/data + rm data/Makefile* + doins data/* +} diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest new file mode 100644 index 000000000000..815385d878f2 --- /dev/null +++ b/sci-biology/treeviewx/Manifest @@ -0,0 +1,13 @@ +AUX treeviewx-0.5.1-70_choose_tree.patch 439 SHA256 99733776abfb7fe3db2ac3dcca5051e8f11f216442206cd7f49d4b7e910a584e SHA512 efe6e903929264359388f88288a95ea28d98efe1eb3dca6248801afa0ab44ee7afdf456f271d088f7b3231b1b9db58c5fde7b147c4ca76b5761d77a1139762bc WHIRLPOOL 9cbec22bfd967592808116ea374f7fac42089be17a56307c83e7b5076a9fa90caf1269a2c3356b8176064a50971dfdd61d0620028a16f3d1dcee5b48c0d6c12d +AUX treeviewx-0.5.1-fix_loading_crash.patch 951 SHA256 13cbf0f6f660fdd54a332aaa13c7ae0f4ee333a8288d98f52ce1a49cf91b2596 SHA512 9c205520dce7851520b24532f88348906c4d5a7f0fe392348099ee9f7377b778792170620856d533a275251a024756482bbd4b83d1da8281b84c39cdf2b3a711 WHIRLPOOL 4b2cd57d9c8f2b88f8075a04e5046865f5bd5a905d5d7c87d6f66dd10efd098926e69af33beea2071129c0fa233dc7477e84aded876beea44e1e7ca798190780 +AUX treeviewx-0.5.1-gcc4.3.patch 2601 SHA256 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2881ec0a4644434320d284a4024f18cba765245de99fa7b50c3cc20ab7a37eb4 SHA512 35f9682bd8f17a2d2436ae6c0b729bcb766fd848b9b24e3f17577e4cef0cd6fd820a8686818feaf6e1414c0f10891bac0befa818a9befc337fd5e87f5120e520 WHIRLPOOL 6f91bd5ebdff8c4c32ff727bf57f2cc122d0034171704650e7263bc7da6cae798b1e4f023526063ecad01f6e69b9e995cdcbfea1478130c086909d2593fcc9e9 +DIST tv-0.5.1.tar.gz 426745 SHA256 118bdbefb3f21636b1ba9da92e1b2029cb4d7d9944f4d02d2deace4ebb14c2d1 SHA512 45a7ac6dff5b22771e4428d6b1ee528c0039956a462658d28d4f588b6df32620d8f69b3bcf5ca23643e2bdd5361da00625fcb1495bcf4f74d44ee22022c63143 WHIRLPOOL 4f115c3a0e4d6ea6205eb4be76413965ed64a1562d8d9a53207cb64e2dce4caff57c430960b402228e1d6515c9797e69162594021c1cdee09028e671a3247c06 +EBUILD treeviewx-0.5.1-r3.ebuild 894 SHA256 06b570db06a8106db648a65e03de33c502e0666e58f798698637b1c358ecdcbf SHA512 316d9b8359813322cf77338aae8b7f687d4a40ca52cd70d739fbf76b28a188e45ac97d430b90fdec2b2c0e081de868cc3c842d0a94a56c8f3d0124eac058ffa9 WHIRLPOOL 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28c429150fb8df5db3205b352f077fe431f3e2ca530195468a340909a3b37882fae67e05452a7810ac34ffb8a02979625b48c28285a7d3abf31004238fce1463 WHIRLPOOL cb576bf37639acbedd4cf7b5bc4ee633e2da958d1a13c674cd29029b5352570791daf3faab3ba010df95499daca19d788d66ce3e621e2ed760ed5ab90b3133bd diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch new file mode 100644 index 000000000000..ed5aa43e23c3 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch @@ -0,0 +1,12 @@ +## 70_choose_tree.dpatch by William Alexander Grant <william.grant@ubuntu.com.au> +--- tv-0.5.orig/tview.cpp ++++ tv-0.5/tview.cpp +@@ -209,7 +209,7 @@ + wxT("SVG vector picture files (*.svg)|*.svg"), + wxSAVE|wxOVERWRITE_PROMPT); + +- if (dialog.ShowModal() == wxID_OK) ++ if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) + { + wxSVGFileDC pictureDC (dialog.GetPath(), 600, 650) ; + OnDraw (&pictureDC); diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch new file mode 100644 index 000000000000..c136539726a3 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch @@ -0,0 +1,40 @@ +Bug: http://code.google.com/p/treeviewx/issues/detail?id=1 +Description: fix crash on loading tree file. +Author: Tim Booth +--- tv-0.5.orig/tview.cpp ++++ tv-0.5/tview.cpp +@@ -278,7 +278,7 @@ + char buf[256]; + strcpy (buf, p->GetLabel().c_str()); + wchar_t wbuf[256]; +- mbstowcs (wbuf, buf, size_t(wbuf)); ++ mbstowcs (wbuf, buf, 256); + s << wbuf; + #else + s << p->GetLabel().c_str(); +@@ -563,7 +563,7 @@ + char buf[256]; + strcpy (buf, t.GetName().c_str()); + wchar_t wbuf[256]; +- mbstowcs (wbuf, buf, size_t(wbuf)); ++ mbstowcs (wbuf, buf, 256); + txt << wbuf; + #else + txt << t.GetName().c_str(); +@@ -712,7 +712,7 @@ + char buf[256]; + strcpy (buf, p.GetIthTreeName(i).c_str()); + wchar_t wbuf[256]; +- mbstowcs (wbuf, buf, size_t(wbuf)); ++ mbstowcs (wbuf, buf, 256); + + std::wstring tname = wbuf; + +@@ -1046,6 +1046,7 @@ + void MyCanvas::OnSize(wxSizeEvent& event) + { + Resize (); ++ Refresh(); + event.Skip(); + } + diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch new file mode 100644 index 000000000000..33bd3b1741f6 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch @@ -0,0 +1,77 @@ +diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp +--- tv-0.5.1/TreeLib/Parse.cpp 2002-02-23 07:22:32.000000000 -0500 ++++ tv-0.5.1.new/TreeLib/Parse.cpp 2008-06-17 06:08:24.000000000 -0400 +@@ -24,6 +24,11 @@ + #include <ctype.h> + #include "Parse.h" + ++ ++ ++ ++#include <cstring> ++ + // Return the next token in the string + tokentype Parser::NextToken () + { +diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp +--- tv-0.5.1/TreeLib/TreeLib.cpp 2004-05-13 08:22:11.000000000 -0400 ++++ tv-0.5.1.new/TreeLib/TreeLib.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -24,6 +24,8 @@ + #include "TreeLib.h" + #include "Parse.h" + ++ ++#include <cstdlib> + #include <vector> + + +diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp +--- tv-0.5.1/TreeLib/treereader.cpp 2003-09-10 08:58:16.000000000 -0400 ++++ tv-0.5.1.new/TreeLib/treereader.cpp 2008-06-17 06:07:15.000000000 -0400 +@@ -28,6 +28,9 @@ + #include <stdlib.h> + #endif + ++#include <cstring> ++#include <cstdlib> ++ + //------------------------------------------------------------------------------ + TreeReader::TreeReader (Tokeniser &p) : parser (p) + { +diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp +--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2002-12-10 06:35:49.000000000 -0500 ++++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,5 @@ ++ ++#include <cstring> + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" +diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp +--- tv-0.5.1/ncl-2.0/src/nexus.cpp 2002-12-10 06:35:50.000000000 -0500 ++++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,5 @@ ++ ++#include <cstring> + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" +diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp +--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2005-04-29 10:28:17.000000000 -0400 ++++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,5 @@ ++ ++#include <cstring> + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" +diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp +--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2001-02-02 07:55:40.000000000 -0500 ++++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,6 @@ ++ ++#include <cstring> ++ + #ifdef __BORLANDC__ + // Undefine __MINMAX_DEFINED so that min and max are correctly defined + #ifdef __MINMAX_DEFINED diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch new file mode 100644 index 000000000000..67a62179bb87 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch @@ -0,0 +1,30 @@ +Author: Olly Betts <olly@survex.com> +Description: Update configure.in to match what it must have said when configure was generated. + One thing I should probably explain about the patch as my change may + seem odd otherwise - upstream's configure.in says "USE_SVG=0" but the + generated configure says "USE_SVG=1", so I've simply updated + configure.in to match what it must have said when configure was + generated. +Forwarded: no +--- tv-0.5.orig/configure.in ++++ tv-0.5/configure.in +@@ -66,7 +66,9 @@ + case "$wx_version" in + 2.4.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_dcsvg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] + ;; +- *) WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] ++ 2.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] ++ ;; ++ *) WX_SVG_LIB= + ;; + esac + +@@ -76,7 +78,7 @@ + + if test "$USE_SVG" = 1 ; then + CXXFLAGS="$CXXFLAGS -DUSE_SVG" +- LIBS="$LIBS -l$WX_SVG_LIB" ++ test -n "$WX_SVG_LIB" && LIBS="$LIBS -l$WX_SVG_LIB" + fi + + AC_OUTPUT(Makefile ncl-2.0/Makefile ncl-2.0/src/Makefile TreeLib/Makefile tv.spec) diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch new file mode 100644 index 000000000000..a57ae19aaf26 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch @@ -0,0 +1,16 @@ +Description: Fix the extension of the icon +Author: Olly Betts <olly@survex.com> +Last-Update: 2014-06-21 +Forwarded: http://code.google.com/p/treeviewx/issues/detail?id=4 + +--- tv-0.5.orig/tv.cpp ++++ tv-0.5/tv.cpp +@@ -215,7 +215,7 @@ + frame->SetIcon(wxIcon("app")); // use the name of the icon in the resource file + #endif + #if defined(__WXGTK__) || defined(__WXMOTIF__) +- frame->SetIcon(wxIcon(wxT("bitmaps/treeview.xbm"))); ++ frame->SetIcon(wxIcon(wxT("/usr/share/pixmaps/treeviewx.xpm"))); + #endif + + #ifdef __WXMAC__ diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch new file mode 100644 index 000000000000..b1db5749990c --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch @@ -0,0 +1,78 @@ + tv.cpp | 4 ++-- + tview.cpp | 12 ++++++++---- + 2 files changed, 10 insertions(+), 6 deletions(-) + +diff --git a/tv.cpp b/tv.cpp +old mode 100755 +new mode 100644 +index 1abe90b..0df45a8 +--- a/tv.cpp ++++ b/tv.cpp +@@ -163,9 +163,9 @@ bool MyApp::OnInit(void) + { + // Optional command line argument is name of file to open + #if wxUSE_UNICODE +- wchar_t *InputFile = NULL; ++ const wchar_t *InputFile = NULL; + #else +- char *InputFile = NULL; ++ const char *InputFile = NULL; + #endif + // Read input/output files + if (argc > 1) +diff --git a/tview.cpp b/tview.cpp +old mode 100755 +new mode 100644 +index 93972c3..4b2d593 +--- a/tview.cpp ++++ b/tview.cpp +@@ -62,9 +62,13 @@ + #ifdef __WXMSW__ + #else + #ifdef USE_SVG ++#if wxMAJOR_VERSION >= 3 ++ #include <wx/dcsvg.h> ++#else + #include <wx/svg/dcsvg.h> + #endif + #endif ++#endif + + // GUI interface + #include "tv.h" +@@ -186,7 +190,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event)) + wxFrame *f = GetMainFrame(); + wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), + pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), +- wxSAVE|wxOVERWRITE_PROMPT); ++ wxFD_SAVE|wxFD_OVERWRITE_PROMPT); + + if (dialog.ShowModal() == wxID_OK) + { +@@ -206,7 +210,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event)) + #endif + wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), + pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), +- wxSAVE|wxOVERWRITE_PROMPT); ++ wxFD_SAVE|wxFD_OVERWRITE_PROMPT); + + if (dialog.ShowModal() == wxID_OK) + { +@@ -361,7 +365,7 @@ bool TView::OnClose(bool deleteWindow) + + // Clear the canvas in case we're in single-window mode, + // and the canvas stays. +-#if (wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated ++#if (wxMAJOR_VERSION >= 3 || wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated + canvas->ClearBackground(); + #else + canvas->Clear(); +@@ -686,7 +690,7 @@ void TView::OnLeafFont (wxCommandEvent& WXUNUSED(event)) + wxFontData data; + data.SetInitialFont (LeafFont); + +-#ifdef __WXMAC__ ++#if wxMAJOR_VERSION >= 3 || defined __WXMAC__ + wxFontDialog dialog((wxWindow *)GetFrame(), data); + #else + wxFontDialog dialog((wxWindow *)GetMainFrame(), &data); diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch new file mode 100644 index 000000000000..2c5179f778ca --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch @@ -0,0 +1,34 @@ +Description: Remove wxSTRING_MAXLEN (removed in wx3.0) and incomp. definition. + The definition wxSTRING_MAXLEN was removed from the public API of wxWidgets. + Its meaning was basically "take all the string", whenever a string length was + expected. The missing definition didn't raise a compilation error because + TreeLib's treedrawer.h contained a fall-back definition, which is however + incompatible with the original definition of wxWidgets and therefore is + interpreted by wxWidgets as a number representing the real string length. + This patch gets rid of the dangerous fall-back definition and of all of its + uses by using alternative wxString constructors that achieve the same + behavior. +Author: Martin Steghöfer <martin@steghoefer.eu> +Last-Update: Sun, 10 Aug 2014 14:06:42 +0200 +Bug-Debian: http://bugs.debian.org/751255 + +--- tv-0.5.orig/TreeLib/treedrawer.cpp ++++ tv-0.5/TreeLib/treedrawer.cpp +@@ -245,7 +245,7 @@ + // error in gcc, which is probably a gcc bug + { + wxCoord w, h, descent; +- wxString s (formatedString.c_str(), wxSTRING_MAXLEN); ++ wxString s (formatedString.c_str()); + pt.x += dc->GetCharWidth(); + pt.y -= dc->GetCharHeight()/2; + dc->DrawText (s, (int)pt.x, (int)pt.y); +@@ -566,7 +566,7 @@ + + #if USE_WXWINDOWS + wxCoord w, h; +- wxString s (buf, wxSTRING_MAXLEN); ++ wxString s (buf); + dc->GetTextExtent (s, &w, &h); + int x = (int)pt2.x; + int y = (int)pt2.y; diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch new file mode 100644 index 000000000000..b1c03bbb39f9 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch @@ -0,0 +1,50 @@ +--- tv.cpp~ 2005-10-01 16:47:35.000000000 -0400 ++++ tv.cpp 2005-10-01 16:52:30.000000000 -0400 +@@ -312,11 +312,15 @@ + { + #ifdef __WXMSW__ + file_menu->AppendSeparator(); +- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile"); ++ file_menu->Append(SAVEAS_PICTURE_CMD, ++ wxT("Save As Picture...")), ++ wxT("Save picture of tree to metafile"); + #else + #ifdef USE_SVG + file_menu->AppendSeparator(); +- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file"); ++ file_menu->Append(SAVEAS_PICTURE_CMD, ++ wxT("Save As Picture...")), ++ wxT("Save picture of tree to SVG file"); + #endif + #endif + file_menu->AppendSeparator(); +--- tview.cpp~ 2005-10-01 16:47:45.000000000 -0400 ++++ tview.cpp 2005-10-01 16:50:42.000000000 -0400 +@@ -184,10 +184,10 @@ + wxString pictureFileName = GetFrame()->GetTitle(); + pictureFileName += wxT(".emf"); + wxFrame *f = GetMainFrame(); +- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, +- "Enhanced metafile (*.emf)|*.emf", +- wxSAVE|wxOVERWRITE_PROMPT); +- ++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), ++ pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), ++ wxSAVE|wxOVERWRITE_PROMPT); ++ + if (dialog.ShowModal() == wxID_OK) + { + wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ; +@@ -204,9 +204,9 @@ + #else + wxFrame *f = GetMainFrame(); + #endif +- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, +- "SVG vector picture files (*.svg)|*.svg", +- wxSAVE|wxOVERWRITE_PROMPT); ++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), ++ pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), ++ wxSAVE|wxOVERWRITE_PROMPT); + + if (dialog.ShowModal() == wxID_OK) + { diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml new file mode 100644 index 000000000000..8683bbc5f8f7 --- /dev/null +++ b/sci-biology/treeviewx/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + TreeView X is a program for displaying phylogenetic trees on Linux and + UNIX platforms. It can read and display NEXUS and Newick format tree + files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other + programs). + </longdescription> +</pkgmetadata> diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild new file mode 100644 index 000000000000..7d1fe1c773e0 --- /dev/null +++ b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +WX_GTK_VER=3.0 + +inherit autotools eutils wxwidgets + +DESCRIPTION="A phylogenetic tree viewer" +HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" +SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/0.5/tv-${PV}.tar.gz" +LICENSE="GPL-2" + +KEYWORDS="amd64 x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/tv-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-wxt.patch + "${FILESDIR}"/${P}-gcc4.3.patch + "${FILESDIR}"/${P}-70_choose_tree.patch + "${FILESDIR}"/${P}-fix_loading_crash.patch + "${FILESDIR}"/${P}-wx30.patch + "${FILESDIR}"/${P}-svg.patch + "${FILESDIR}"/${P}-treeview-xpm-not-xbm.patch + "${FILESDIR}"/${P}-wxstring-maxlen.patch + ) + +src_prepare() { + epatch "${PATCHES[@]}" + mv configure.{in,ac} || die + eautoreconf +} diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest new file mode 100644 index 000000000000..2f645f711eb3 --- /dev/null +++ b/sci-biology/trf/Manifest @@ -0,0 +1,5 @@ +DIST trf404.linux 89853 SHA256 1b9e3917088684afc2287a078810858f7a8e50d90e7bad2d814d40dc24188058 SHA512 c1aa05e394d47ea153df3082258f9a089aa59976963e9ac5d5816ef9dcd95c47e2e46861d1b2aae52b5ea9950a823a2449dd0d8426b04f2b738f5552c319393e WHIRLPOOL 7817c7eeb2c452ece7f71c2b7548fd9cda8c6796d5e77b2de46911f50bb271290b1a9601545efc50b94574c718e0e5e65d4a4e27f5cfd66c3590e9d5b7c5856c +EBUILD trf-4.04-r1.ebuild 623 SHA256 b346b25b99ffa5990102ab3a8c921404e4d6d7e424b59003050d7b2a88510c44 SHA512 a879d5171ebbb5fff9157d05c7f8413044758be60a5d4d790d779f65d3c8b16ac72a9a942f12f651576bd5082e1cb1171471f9886e5eba459903b473a7b07af1 WHIRLPOOL 512b7a588f8505d4742e88f89037322dcd0c3121069c6a688bf57aaea930c2bf64bd4202b26697c2a3893bb3d16c1d39b929dd0b5f803e35f6356fa10ef15a3b +MISC ChangeLog 2416 SHA256 411baa5e2565766402bbd39fd80dc884eb854a84b05b882356e4afc1d4f1de7e SHA512 bd45cbc13d034e66553ae70abfecc146ce49e56b3103590f1a24fcc045f5731c0f0b58ae3202a8d26254963a788406e09aff252006c33c86f5af456ff6f1f96f WHIRLPOOL 53a3cb4d34cb38d261a2d272a4e0beabc4933d0dd1fff16744e59b74f82c1c4cc6223cd2db24a70d7e6dd2e5fc27e792619b1fcb3dccb70798fac0faa786d64a +MISC ChangeLog-2015 1376 SHA256 87b6f967a822321f462017150f16dbb7d9f3219468eb193315fae628cc43bd46 SHA512 254398e6d9ca058c12a8e718afaec9485c673c9a7b9be8d3b51091b12bdd3921b1b550a41798bf9d9cc3ee4fb8250b46677c67e7f9b244ff3804e6f5ad619a7f WHIRLPOOL 0f33cef06dd3cc14921f74dc89e9ab5244fce5fdeb3d09bd2e7fee869f72c692b6e0f10ac8497caffb5adc3fb0518b06b727eee64c25fdd94bceaf82ecf70dd0 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/trf/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/trf/trf-4.04-r1.ebuild b/sci-biology/trf/trf-4.04-r1.ebuild new file mode 100644 index 000000000000..3b906fb31aaf --- /dev/null +++ b/sci-biology/trf/trf-4.04-r1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_P="${PN}404" + +DESCRIPTION="Tandem Repeats Finder" +HOMEPAGE="http://tandem.bu.edu/trf/trf.html" +SRC_URI="http://tandem.bu.edu/trf/downloads/${MY_P}.linux" + +LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html +SLOT="0" +KEYWORDS="amd64 x86" +RESTRICT="mirror bindist" + +S=${WORKDIR} + +QA_PREBUILT="opt/${PN}/.*" + +src_unpack() { + cp "${DISTDIR}/${MY_P}.linux" "${S}/${MY_P}.linux.exe" || die +} + +src_install() { + exeinto /opt/${PN} + doexe trf404.linux.exe + dosym /opt/${PN}/${MY_P}.linux.exe /opt/bin/trf +} diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest new file mode 100644 index 000000000000..d5df13d2c367 --- /dev/null +++ b/sci-biology/trnascan-se/Manifest @@ -0,0 +1,8 @@ +AUX trnascan-se-1.23-glibc-2.10.patch 6702 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42 SHA512 2df0a5d6bf633b9b1c1ccce002c5a751a3f5c5eedf755b24a3af1a6d07a93816b6be4195aa3142ebcbd16ad9b373223f398fbac1d91769b26be1d295f080f181 WHIRLPOOL d8bc3d22d50446ffc628276261d091cb0552e564c0d80c9c6fe6e4108c3c036a11fadd48c45a115fef56ac01a49df0b7a0cebb026fcff05344822c29b074f971 +AUX trnascan-se-1.23-ldflags.patch 971 SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9 SHA512 bcfdc71dc8454e110d45f44bf9c4a0b4e77ca85bcf0b501dd2de60c47418bc5d442b1ac976c6a333eb4398a12e4478b8817436246a1f872df208d5eaf64c3ac2 WHIRLPOOL f1afc811efcc061a114ab6b14ac2ef4ce8c7091bdfa6a392ac55dd6f1e38f1d1ded94f218309e2e3abd515ef80bffbefd7e4ed30d993e16603c0477b988f48b3 +AUX trnascan-se-1.31-ldflags.patch 973 SHA256 e103841dfe3f289493c80fc938a3c9318a550e160b3269b9856405ee48dc648a SHA512 ff677ce9ac3ed9299f6a3bf977642e2a6c300a1b801436bb5d3787968cfe28357a0ec23d0438f0b15c06324cd7e1bbbda590c8fb5574577a3f653779316931df WHIRLPOOL 2ba11012cd414d2dc9a523109bfebe726a347558cf1098f52410fc88c652665e6babeaef5581dce12fdd1a83af8ed417d8040ef481d5036a9632838f997333c2 +DIST trnascan-se-1.31.tar.gz 740960 SHA256 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d WHIRLPOOL aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665 +EBUILD trnascan-se-1.31.ebuild 1191 SHA256 f70623b4b41a9efe071bb98865a3eb1ecc67293f42371d32ed118c47c3fb6ebb SHA512 d79fa9d244d4f3ab98fff94aca074bd23cc953c0b812a270daca2e80c440fcdcfd38e92cba2eea6ccd2ad9873c8fb898f46b9f4356c638d01fa0f2b21e23c55b WHIRLPOOL 564cd24e354568dfcedf143fe6a60746ee282c334e6ee20fde196803cf57a237c52913be7be1ef559b0403bdb8676cc9bb3429e4f9f27dcd4b71b6c5c8f4527b +MISC ChangeLog 2630 SHA256 c56279b0e6cc8f7d84de536b5b3c6a8b152ead15a41f8a2927ef13a0691251e3 SHA512 d1a2dd013269faa1608f1015ff965ffe35c56df2001a6be7a64d6e5589c20dbf4e3b3732d3696e06ac08c78eb7933dd2736c293f5a591854375db76967524c2e WHIRLPOOL e25bad73167056904784b8b236615c58f1f2e107727265139147950600daf703ba2bd55453977f4cba2ae9fb416ef392625fa07ac25868664ccaefcf303b5673 +MISC ChangeLog-2015 2136 SHA256 c029d5251ef50292b150acebe84c985fc78797e026570389855ec6f5d48243a9 SHA512 5163d5de7b8962b0b744bf632db8cc3614970ae792c04d423f8a016c6757a8583053e05836fabb8dfb7bf2e78cba2d872fa18438689d2bcbbcaaedd9d7009472 WHIRLPOOL 90cc0c3fc4dcecb496558acb97b0e1c5f529c9dc4d1b05a2533991560b4d448927f945226b12f581b39bfbe05b86f068b3430368bfcb384e3384b499091a3b11 +MISC metadata.xml 608 SHA256 f64eaf62ed800ea168869df240fc649a3141d18509ca545d46577656a74d83cf SHA512 d94549c3878aa8a32f107bfe2cebb07e9965b61fe2cfa030211b98db2e98b2aad71e5e4e7fbeb97ba2767f6a0dc244992045da13560c2e3f3cad3044a86ef826 WHIRLPOOL d7bf3b4559c5082f7c5963c9b71fb4ca746fb5cf107b5f550478cd4fbeba763f1db2dd5fb645e5d18fe7ebd38e72fb66a26e9f43e25b6fb8052da7b74f59ca43 diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch new file mode 100644 index 000000000000..e21da6e58db0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch @@ -0,0 +1,292 @@ +diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c +--- trnascan-se-1.23.orig/sqio.c 2002-04-12 23:12:04.000000000 +0300 ++++ trnascan-se-1.23/sqio.c 2009-08-05 21:45:53.000000000 +0300 +@@ -235,7 +235,7 @@ + } + + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + readline(V->f, V->sbuffer); + } +@@ -306,7 +306,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + done = feof(V->f); + done |= (*endTest)(V->sbuffer, &addend); + if (addend || !done) +@@ -332,7 +332,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -341,7 +341,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -350,7 +350,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -364,7 +364,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -382,7 +382,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -394,7 +394,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -416,7 +416,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -425,7 +425,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -443,7 +443,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -454,7 +454,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -487,11 +487,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -521,12 +521,12 @@ + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); + +- getline(V); /*skip title-junk line*/ ++ get_line(V); /*skip title-junk line*/ + + readLoop(0, endNBRF, V); + + while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>'))) +- getline(V); ++ get_line(V); + } + + +@@ -559,7 +559,7 @@ + } else Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -579,7 +579,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -625,7 +625,7 @@ + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -652,7 +652,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -661,7 +661,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -685,7 +685,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -701,7 +701,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -712,7 +712,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -734,7 +734,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -746,7 +746,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -754,7 +754,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -786,14 +786,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -801,7 +801,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -848,7 +848,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -862,7 +862,7 @@ + SeqfilePosition(SQFILE *sqfp, long offset) + { + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -954,7 +954,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch new file mode 100644 index 000000000000..783e4340823d --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index 53e5c5b..a2d3feb 100644 +--- a/Makefile ++++ b/Makefile +@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o + all: $(PROGS) tRNAscanSE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + + trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c + + tRNAscanSE: + $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch new file mode 100644 index 000000000000..f28b1e8f6bb0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index 53e5c5b..a2d3feb 100644 +--- a/Makefile ++++ b/Makefile +@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + + trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c + + tRNAscan-SE: + $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml new file mode 100644 index 000000000000..ab96459c84db --- /dev/null +++ b/sci-biology/trnascan-se/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA + genes, with a false positive rate of less than one per 15 gigabases, + and with a search speed of about 30 kb/second. It was implemented for + large-scale human genome sequence analysis, but is applicable to + other DNAs as well. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild new file mode 100644 index 000000000000..cd8dc152d6d2 --- /dev/null +++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit perl-functions toolchain-funcs + +DESCRIPTION="tRNA detection in large-scale genome sequences" +HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" +SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S="${WORKDIR}"/tRNAscan-SE-1.3.1/ + +PATCHES=( + "${FILESDIR}"/${P}-ldflags.patch +) + +src_prepare() { + default + sed \ + -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \ + -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \ + -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \ + -i Makefile || die + + perl_set_version +} + +src_test() { + emake PATH="${S}:${PATH}" testrun +} + +src_install() { + dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 + + newman tRNAscan-SE.man tRNAscan-SE.man.1 + + dodoc MANUAL README Release.history + + insinto /usr/share/${PN}/ + doins *.cm gcode.* Dsignal TPCsignal + + dodoc Manual.ps + + insinto ${VENDOR_LIB} + doins -r tRNAscanSE +} diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest new file mode 100644 index 000000000000..8ff452aaf20e --- /dev/null +++ b/sci-biology/uchime/Manifest @@ -0,0 +1,6 @@ +AUX CMakeLists.txt 549 SHA256 56ab311986a4ebf20dc8a0929d0ab1820233c0a81e7802b40ee683cf64895031 SHA512 02b43fbfa0a8fd9e5389033e5a8b97d356dfc2d29d076539eea5830b30526745014bc1eab302ccb8fd27b65a1afd92537b94c3c266a4b285de1b7a287fa8a867 WHIRLPOOL 8fa3739e15061160c78174c43f8b029ba46c1f892e3bc5686f4dca306f72bcbc3f96acfedb670db5c8b11ab642740e26f58860a83c148a7b8e1bc11927943016 +DIST uchime4.2.40_src.tar.gz 66772 SHA256 cb6a3aea4e8b4343a6e0ddde3b2755bbec53492bae5d6252ce8a7091061f353d SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b WHIRLPOOL 28ad19892ac8b4db03e93fd1fca39b05d6675c241a97f7a2ab241765589b34c56684ab4923eaf568a5f9b0e1583ce1460be7f0edf9d9201e5d3db3da0efb0ee6 +EBUILD uchime-4.2.40.ebuild 500 SHA256 b727045e5b473bb10d9af55201c54c4197937fa8358aa7521fecd0af249fd5ea SHA512 5e5757f0fb4de458662828805fc8b2d63573a450c7b6f5249f05103061f6f577ea91d7ec1fdea6889c3690647c536f79b35894e9d99040e12e111c2436b4c258 WHIRLPOOL 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641d91bff3651a49a3b7e15260cf2a758199ae49ece16643d3104f0f4e202938935edeb3bef18f7afc40a4eb1b1b3e469b07fec95d30a5e686e4b66535ff3e7e WHIRLPOOL 1994686e308ee6704205946dd8c3a7be908b941e21847d7098eac2f62ca2a511c3789f39a623950623fe54f15601217a8a3a5aacfaf36524ae4749e6cf0efa76 diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt new file mode 100644 index 000000000000..54b0a3ba0d30 --- /dev/null +++ b/sci-biology/uchime/files/CMakeLists.txt @@ -0,0 +1,11 @@ +cmake_minimum_required(VERSION 2.6) +project(UCHIME) + +set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1") + +# Simply copy the source files from the mk script +add_executable(uchime + addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp) + +INSTALL(TARGETS uchime + DESTINATION bin) diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml new file mode 100644 index 000000000000..8e8ff4997171 --- /dev/null +++ b/sci-biology/uchime/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> +UCHIME is a new algorithm for detecting chimeric sequences. It was developed in +collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob +Knight. Chimeras are commonly created during DNA sample amplification by +PCR, especially in community sequencing experiments using single regions +such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can +detect chimeras using a reference database or de novo using abundance +information on the assumption that chimeras are less abundant than their +parents because they must have undergone fewer rounds of amplification. +</longdescription> +</pkgmetadata> diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild new file mode 100644 index 000000000000..dd2201547ae0 --- /dev/null +++ b/sci-biology/uchime/uchime-4.2.40.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +MY_P="${PN}${PV}_src" + +DESCRIPTION="Fast, accurate chimera detection" +HOMEPAGE="http://www.drive5.com/uchime/" +SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="debug" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + + cmake-utils_src_prepare +} diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest new file mode 100644 index 000000000000..9b21e29f6f4b --- /dev/null +++ b/sci-biology/ucsc-genome-browser/Manifest @@ -0,0 +1,5 @@ +DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248 +EBUILD ucsc-genome-browser-260.ebuild 2920 SHA256 d88b2c78291cc64137193b4a300aae814b488721f6326f78c53f84948730b2e1 SHA512 4b9f58349249201f35454c99a1e1e35f3aa5bd4a1477fb534b8843bec52212768859b85c0e14aece50a02b2920c297ed96717d13a111583ed023f59b00481f7a WHIRLPOOL 92e470312ad45d04fbb09a780b72aec6b591e84b3b66c85b0c7716f4edfbfc823fd8a2500167ee4ab10d4e7dd4d1c877337aed2f2d876af9c1bb3843f8cce65c +MISC ChangeLog 2462 SHA256 f0197213b438d3f1ddd7a9c8933f488201638602b1b81edf833ef7c3374e3a92 SHA512 0bf627625bb844f013b3f15ee03bd151ea482e641def0a606f35c097763b7ee3bc95fd33d859921cc31b36b015f61282459bedbe8da487f361b5103ff985b426 WHIRLPOOL e22226d2842233abfaa4abcc7e6c937600cd77dd05a9fa85992360047b03736b73c67eff24fd8a04ae7272193421427ab5efad59a21deaa680bffac2f488d36a +MISC ChangeLog-2015 1543 SHA256 e4528cb56770a7989b4c681b2ca915691d1c4efde053d96bb152ed077ec5bbf8 SHA512 e4f17c85b1df30b7277271edc19409cd9062a64704023ff975ef51321428e3bdae035f1f5f487ebadfa1eef4fc6e3cae2aa788d57b68c27875e88465e7f1c6fc WHIRLPOOL fd8bceba956dd2506377ba6748f43a4fbbb753b35e7bd2397b0955a840b32b20a643d5f4498d2f05acc71094e51523f29f08c3b6e129eb9712fc7ac1791014eb +MISC metadata.xml 435 SHA256 937efe8e0861e55f1d8d4aa0d431e262657c10e3476041113f6561aee3290a59 SHA512 1acffee210c77abc41a93b5b78e52b27ed18df50a2eff3c6463e34bc031a4b2c97d1472a0dcf14bbf513c77d930a67434194c2e5ac435a5f7fd1e79294335a81 WHIRLPOOL 7601aae3dd7ebbc856edc983a0b2a38fe8687c52af40065fea816e09778be45311182468a72fd9078489ca49634d2e41263ada07b088ea626b577bb95bdaba31 diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml new file mode 100644 index 000000000000..042f7b949ba9 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild new file mode 100644 index 000000000000..7ce025b2ae95 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs flag-o-matic webapp + +DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath" +HOMEPAGE="http://genome.ucsc.edu/" +SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip" + +LICENSE="blat" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+mysql +server static-libs" + +REQUIRED_USE="server? ( mysql )" + +WEBAPP_MANUAL_SLOT="yes" + +DEPEND=" + app-arch/unzip + !<sci-biology/ucsc-genome-browser-223 + mysql? ( virtual/mysql ) + server? ( virtual/httpd-cgi )" # TODO: test with other webservers +RDEPEND="${DEPEND}" + +S="${WORKDIR}/kent" + +src_prepare() { + use server && webapp_src_preinst + sed \ + -e 's/-Werror//' \ + -e "/COPT/s:=.*$:=${LDFLAGS}:g" \ + -e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \ + -e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \ + -i src/inc/common.mk src/hg/lib/makefile || die + find -name makefile -or -name cgi_build_rules.mk \ + | xargs sed -i \ + -e 's/-${USER}//g' \ + -e 's/-$(USER)//g' \ + -e 's:-O2::g' \ + -e 's:-ggdb::g' \ + -e 's:-pipe::g' || die + sed \ + -e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \ + -i src/hg/genePredToMafFrames/makefile || die +} + +src_compile() { + export MACHTYPE=${MACHTYPE/-*/} \ + BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \ + SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \ + ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \ + PATH="${BINDIR}:${PATH}" \ + STRIP="echo 'skipping strip' " + + export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" + + use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ + MYSQLINC="${ROOT}usr/include/mysql" + + use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ + CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" + + mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die + use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT" + + emake -C src clean + emake -C src/lib + emake -C src/jkOwnLib + emake -C src/utils/stringify + emake -C src blatSuite + if use mysql; then + emake -j1 -C src/hg utils + emake -j1 -C src utils + emake -C src libs userApps + if use server; then + emake -j1 -C src/hg + emake -j1 -C src + fi + fi +} + +src_install() { + use server && webapp_src_preinst + cp -ad "${WORKDIR}"/destdir/* "${D}" || die + use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a + echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}" + doenvd "${S}/98${PN}" + + use server && webapp_postinst_txt en src/product/README.QuickStart + use server && webapp_src_install + + insinto "/usr/include/${PN}" + doins src/inc/*.h + insinto "/usr/share/${PN}" + doins -r src/product + keepdir "/usr/share/doc/${PF}" + find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die +} + +pkg_postinst() { + use server && webapp_pkg_postinst +} diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest new file mode 100644 index 000000000000..ff0522bee054 --- /dev/null +++ b/sci-biology/unafold/Manifest @@ -0,0 +1,5 @@ +DIST unafold-3.8.tar.bz2 282418 SHA256 7552724ce82ad8618167ec0524d8c931ac4383314669322c8424cafc06c2bf38 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c WHIRLPOOL 9fd5744e66d8669817433b5427fc671ac5185760ffaf0682a7938fc5542f24cbe7b08f7722c7135cd3197af2d748740e0ca35a70a5f6c40a4a5d5aaa806ed923 +EBUILD unafold-3.8-r1.ebuild 589 SHA256 a0483fe9069ef4cde39ee2669da9f611996b4e3b6feeb0cec99529089c53b9e3 SHA512 4b025f8e4b52ef5e833d299973d44e5846000c45b7f36f200dc14414cb1367188f228e8fba23782f19475a38eb6f6d1cf8ca053b5d70f8b573aee69da7fc71b9 WHIRLPOOL ca9b77fa995b1fbdff8fa0db79db45b01690f7acc0e2e95885c0964b495da70f2cfadfcc6c352a55aed4134f601d167c664300ca0950f2eaf3818dc7422aa4ba +MISC ChangeLog 2480 SHA256 b82760c0782b0cf2d63fa7262ebc67acfebc94bafdf670ae0c3efa8a317f8d3d SHA512 52f440da912fd1ede230984fa5748085e20bebbf2e484e7f28b165e2ed7f4ea28895e557d1122e844ba3da7d9b754c29e4f334b8f6b1698b18090163dd4da194 WHIRLPOOL 920c020275a5767432eacbe749a6dda767944ea0ac896270ac7c0f0a207f800e5aef2ac131487b113d9f94ed9dc70005660226104af5de14e4fba92c9b397794 +MISC ChangeLog-2015 677 SHA256 affcd65b3c6d414a960ec6c4f7052f189add7c83da5f91623383cf15b3f8e607 SHA512 f0c77df86c9f95155c0fd724b0350a217d5dcf6c83aa7c0d273c39026ad321b7c57d018e7c33891482885c5d6d5d934a45063d542c29ef05c3a70762f20b432a WHIRLPOOL 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a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild new file mode 100644 index 000000000000..e4fff4e8cabd --- /dev/null +++ b/sci-biology/unafold/unafold-3.8-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit flag-o-matic + +DESCRIPTION="Unified Nucleic Acid Folding and hybridization package" +HOMEPAGE="http://mfold.rna.albany.edu/" +SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2" + +LICENSE="unafold" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="custom-cflags" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare() { + # recommended in README + use custom-cflags || append-flags -O3 + + sed \ + -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \ + -i tests/hybrid.tml || die +} diff --git a/sci-biology/update-blastdb/Manifest b/sci-biology/update-blastdb/Manifest new file mode 100644 index 000000000000..5fe3c3949c52 --- /dev/null +++ b/sci-biology/update-blastdb/Manifest @@ -0,0 +1,5 @@ +DIST ncbi_cxx--12_0_0.tar.gz 37925914 SHA256 432d5c72cc02dad263f1b2f1ab875e04e60b1ded0c5537ed54e8095b50554d20 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed WHIRLPOOL 16f0b6de7e0d898bca7a2a46a64a4aa0795f99673d4715a21cca2dc5aa728143b56f02ad9c108543195a8f86f4267777d2be9428dcf52f5495083a63961ad867 +EBUILD update-blastdb-12.0.0.ebuild 654 SHA256 0ea57d56b043c576ad20fedad07c20d3d5b17bf59bde79ada412417c85fccda4 SHA512 3d83521ff73cb97d9f816b61e0aa30ceb690b4720d3486d1c377c9d4da7bb168d22e43d40ce3edd85dd1d7a8a133084734895223a0eb3ea5b7bf420d093ddb92 WHIRLPOOL 14613944758a6b804f37796e3981135ff4c019c883b3ef16fe969e00a25baa83173900d9e9c5b4ddb12dc0d4b2d53be728056110861ab98b4ff66abf4d267dad +MISC ChangeLog 2453 SHA256 1a72fe00f0710fba0dd3df19685c7cffb50c0555b96472b04fb87c5259c08275 SHA512 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d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/update-blastdb/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild new file mode 100644 index 000000000000..e1524b487a03 --- /dev/null +++ b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit versionator + +MY_PV="$(replace_all_version_separators _)" + +DESCRIPTION="update_blastdb.pl for local blast db maintainance" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" +SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-lang/perl + !sci-biology/ncbi-tools++" +DEPEND="" + +S="${WORKDIR}" + +src_install() { + dobin ncbi_cxx--${MY_PV}/src/app/blast/update_blastdb.pl +} diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest new file mode 100644 index 000000000000..077dc3dfa2a9 --- /dev/null +++ b/sci-biology/vaal/Manifest @@ -0,0 +1,7 @@ +AUX vaal-46233_remove-namespace-std.patch 23667 SHA256 24b54021fe8deb7655162779cbf0d9e9c6ab07dbca806b04085dcf9313d6db7c SHA512 47df9a497541d18d96ec6314288e8a429c1d71030f61f8bc29f1a95292f1f2bf53aedd88a16666c204f3bea051b7521ca13de6d03f52f78fcbc5d1cf24a76c47 WHIRLPOOL c5f868ec2041a9413a353ee89ce3346cd51df1b64920e69b92e61ddfc585a20bd7c53f7473605bb91560b544d5f3f81c8a5468dbc8f4df3555a35d8d50403485 +DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175 +DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL 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d508d48c7ed2f65219275f70720df978e3874b430b64aaed3833a6aae7821e0d5f3d5c0cc5478033cec30c533e3c6cfddbc1f5da48be797ce927ace0a70ed99d WHIRLPOOL 7e6ff98b96049a0cc09c72eb8a30f577257f26995351c3095dbe9d71f683466efeebde6bfd012b0d7d398e044c9f3187faf29f35f35dbba0624d3cc61cc029b4 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch new file mode 100644 index 000000000000..c3c3ec032481 --- /dev/null +++ b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch @@ -0,0 +1,911 @@ +Remove 'using namespace std' causing massive havoc with newly +introduced std::align in GCC-5. Fix bug +https://bugs.gentoo.org/show_bug.cgi?id=568438 + +--- vaal-46233/src/efasta/EfastaTools.cc ++++ vaal-46233/src/efasta/EfastaTools.cc +@@ -18,6 +18,8 @@ + #include "math/Functions.h" + #include "math/Array.h" + ++using std::set; ++ + #define Err(message) \ + { cout << message << endl << "\nInvalid.\n" << endl; \ + TracebackThisProcess( ); } +--- vaal-46233/src/Equiv.cc ++++ vaal-46233/src/Equiv.cc +@@ -9,6 +9,8 @@ + #include "Equiv.h" + #include "Vec.h" + ++using std::swap; ++ + bool equivalence_relation::equiv(int a, int b) const + { if ( a == b ) return true; + int c = a; +--- vaal-46233/src/FastaFilestream.cc ++++ vaal-46233/src/FastaFilestream.cc +@@ -13,6 +13,8 @@ + + #include <strstream> + ++using std::string; ++ + template <typename vecT, typename seqT, typename convT, typename verifT> + FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename, + FastaNameParser* name_parser ) +--- vaal-46233/src/FastaFilestreamPreview.cc ++++ vaal-46233/src/FastaFilestreamPreview.cc +@@ -11,6 +11,8 @@ + + #include <algorithm> + ++using std::streamoff; ++ + FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream) + : max_sequence_size_(0), start_offset_(0) + { +--- vaal-46233/src/FastaFilestreamPreview.h ++++ vaal-46233/src/FastaFilestreamPreview.h +@@ -12,6 +12,8 @@ + + #include "Vec.h" + ++using std::streampos; ++ + // FastaFilestreamPreview understands just enough about the fasta + // format to be able to count the number of sequences in the specified + // filestream and to know where each sequence starts in that filestream. +--- vaal-46233/src/Fastavector.cc ++++ vaal-46233/src/Fastavector.cc +@@ -14,6 +14,8 @@ + #include <istream> + #include <string> + ++using std::max; ++ + // Split this into chunks, separated by gaps ('n'), and return each chunk as a + // gapless fastavector. + // TODO: generalize this into a templatized STL algorithm. +--- vaal-46233/src/Fastavector.h ++++ vaal-46233/src/Fastavector.h +@@ -24,6 +24,9 @@ + #include <iostream> + #include <unistd.h> + ++using std::string; ++using std::istringstream; ++ + typedef std::tuple<String, int, int> FastaRegion; + + class fastaindex { +--- vaal-46233/src/FetchReads.cc ++++ vaal-46233/src/FetchReads.cc +@@ -36,6 +36,8 @@ + #include "Qualvector.h" + #include "random/Random.h" + ++using std::istringstream; ++ + // Heuristic constants: + + namespace +--- vaal-46233/src/feudal/BaseVec.cc ++++ vaal-46233/src/feudal/BaseVec.cc +@@ -21,6 +21,7 @@ + using std::ostream; + using std::cout; + using std::endl; ++using std::max_element; + + // Cap: in a given basevector, replace any sequence of N > n identical + // bases by n of the same base. +--- vaal-46233/src/graph/Digraph.cc ++++ vaal-46233/src/graph/Digraph.cc +@@ -16,6 +16,8 @@ + #include "graph/Digraph.h" + #include "math/Functions.h" + ++using std::make_pair; ++ + Bool digraph::HasEdge( int v, int w ) const { + return find( from_[v].begin(), from_[v].end(), w ) != from_[v].end(); + } +--- vaal-46233/src/graph/DigraphTemplate.h ++++ vaal-46233/src/graph/DigraphTemplate.h +@@ -34,6 +34,8 @@ + #include "graph/Digraph.h" + #include <cstddef> + ++using std::make_pair; ++ + template<class E> vec<int> digraphE<E>::EdgesConnectedTo( const vec<int>& v ) const + { vec<int> G = VerticesConnectedTo(v), e; + for ( int x = 0; x < G.isize( ); x++ ) +--- vaal-46233/src/IndexedAlignmentPlusVector.cc ++++ vaal-46233/src/IndexedAlignmentPlusVector.cc +@@ -9,6 +9,8 @@ + #include "IndexedAlignmentPlusVector.h" + #include "VecAlignmentPlus.h" + ++using std::streamoff; ++ + // These strings are at the head of the vector and index files for verification purposes. + + const String VecAlignmentPlusHeaderIO::mStrVectorHeader( "alignment_plus vector V.2\n" ); +--- vaal-46233/src/IndexedAlignmentPlusVector.h ++++ vaal-46233/src/IndexedAlignmentPlusVector.h +@@ -15,6 +15,7 @@ + + #include "Alignment.h" + ++using std::streampos; + + // This class encapsulates the header information for both vectors and indices. + +--- vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc ++++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc +@@ -10,6 +10,7 @@ + #include "kmers/KmerParcels.h" + #include "system/WorklistN.h" + ++using std::fixed; + + inline String Tag(String S = "KPs") { return Date() + " (" + S + "): "; } + +--- vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h ++++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h +@@ -6,6 +6,9 @@ + // Institute is not responsible for its use, misuse, or functionality. // + /////////////////////////////////////////////////////////////////////////////// + ++using std::hex; ++using std::dec; ++ + // --------------------------------- + // NaifTimer + // --------------------------------- +--- vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h ++++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h +@@ -10,7 +10,7 @@ + #ifndef KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H + #define KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H + +- ++using std::map; + + // -------------------------------------- + // MapOfCounters +--- vaal-46233/src/layout/ContigActualloc.h ++++ vaal-46233/src/layout/ContigActualloc.h +@@ -17,6 +17,8 @@ + #include "system/Crash.h" + #include "Misc.h" + ++using std::set; ++using std::map; + + // + // Class contig_actualloc +--- vaal-46233/src/lookup/ImperfectLookup.h ++++ vaal-46233/src/lookup/ImperfectLookup.h +@@ -52,6 +52,8 @@ + #include "lookup/AlignCollector.h" + #include "solid/Solid.h" + ++using std::unique_ptr; ++ + class TaskTimer; + + +@@ -534,7 +536,7 @@ + aligns.resize( nqueries ); + } + +- auto_ptr<TaskTimer> t1, t2; ++ unique_ptr<TaskTimer> t1, t2; + + if ( m_instr_level & IO_TIMER != 0 ) t1.reset( new TaskTimer() ); + if ( m_instr_level & CPU_TIMER != 0 ) t2.reset( new TaskTimer() ); +--- vaal-46233/src/lookup/LookAlign.cc ++++ vaal-46233/src/lookup/LookAlign.cc +@@ -29,6 +29,8 @@ + #include "random/Random.h" + #include "system/ParsedArgs.h" + ++using std::istrstream; ++ + String QUERY("QUERY"); + + void look_align::ResetFromAlign(const align & al, const basevector & b1, +--- vaal-46233/src/lookup/LookAlignFinder.h ++++ vaal-46233/src/lookup/LookAlignFinder.h +@@ -12,6 +12,8 @@ + #include "lookup/LookAlign.h" + #include "Vec.h" + ++using std::set; ++ + /** + Class: LookAlignFinder + +--- vaal-46233/src/lookup/LookAlignSort.h ++++ vaal-46233/src/lookup/LookAlignSort.h +@@ -15,6 +15,8 @@ + + #include <functional> + ++using std::set; ++ + /// Read in look_aligns from file, sort, and load into vecs + /// \param fname name of look_align text file + /// \param aligns vector into which to put the alignments +--- vaal-46233/src/lookup/LookupTable.h ++++ vaal-46233/src/lookup/LookupTable.h +@@ -18,6 +18,8 @@ + + #include <set> + ++using std::set; ++ + typedef pair<unsigned int, unsigned int> LocSeq; + + /// +--- vaal-46233/src/lookup/QueryLookupTableCore.cc ++++ vaal-46233/src/lookup/QueryLookupTableCore.cc +@@ -456,6 +456,9 @@ + #include "system/ParsedArgs.h" + #include "system/file/FileReader.h" + ++using std::istrstream; ++using std::less_equal; ++ + #define ABORT(MSG) \ + { out << MSG << " Abort." << endl << endl; \ + exit(1); } +--- vaal-46233/src/lookup/ShortQueryLookup.cc ++++ vaal-46233/src/lookup/ShortQueryLookup.cc +@@ -32,6 +32,8 @@ + #include "lookup/AlignCollector.h" + #include "lookup/ImperfectLookup.h" + ++using std::ios_base; ++ + // Run an alignment processing chain: seqs -> look -> receiver -> aligns + // That is, look turns seqs into hits, which receiver accepts + // and turns into alignments which are passed to aligns. The +--- vaal-46233/src/Map.h ++++ vaal-46233/src/Map.h +@@ -21,7 +21,7 @@ + #include <map> + #include <ext/hash_map> + using namespace __gnu_cxx; +- ++using std::map; + + ///Return true if k is a key in map m + template<class Key, class Value, typename Cmp> +--- vaal-46233/src/math/Array.h ++++ vaal-46233/src/math/Array.h +@@ -12,6 +12,9 @@ + #include "CoreTools.h" + #include "Vec.h" + ++using std::map; ++using std::fill; ++ + // ============================================================================== + // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> > + // The elements are uninitialized. +--- vaal-46233/src/math/Functions.cc ++++ vaal-46233/src/math/Functions.cc +@@ -10,8 +10,8 @@ + #include "STLExtensions.h" + #include "math/Functions.h" + +- +- ++using std::isfinite; ++using std::make_pair; + + /* CombineNormalDistribution Filipe Ribeiro 2009-06-22 + * +--- vaal-46233/src/math/Functions.h ++++ vaal-46233/src/math/Functions.h +@@ -14,6 +14,10 @@ + #include <cmath> + #include <numeric> + ++using std::min; ++using std::cerr; ++using std::swap; ++ + // =========================================================================== + // + // Min functions +--- vaal-46233/src/math/HoInterval.cc ++++ vaal-46233/src/math/HoInterval.cc +@@ -10,6 +10,8 @@ + #include "math/HoInterval.h" + #include "STLExtensions.h" + ++using std::make_pair; ++ + bool ho_interval::Merge(const ho_interval & o) { + if (!Meets(*this,o)) return false; + *this = Span(*this, o); +--- vaal-46233/src/math/HoInterval.h ++++ vaal-46233/src/math/HoInterval.h +@@ -14,6 +14,8 @@ + #include "feudal/MasterVec.h" + #include "feudal/SerfVec.h" + ++using std::max; ++ + /// Class: ho_interval + /// A half-open interval [a, b). + class ho_interval { +--- vaal-46233/src/PackAlign.h ++++ vaal-46233/src/PackAlign.h +@@ -133,6 +133,8 @@ + #include "pairwise_aligners/Mutmer.h" + #include "feudal/BinaryStream.h" + ++using std::make_pair; ++ + const int Bits2 = 3, Bits3 = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, + Bits16 = 65535; + +--- vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc ++++ vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc +@@ -19,6 +19,9 @@ + #include "pairwise_aligners/AlignFromMutmers.h" + #include "pairwise_aligners/SmithWatBandedA.h" + ++using std::map; ++using std::set; ++ + // If there's a perfect match of length at least perf but we produced no proper + // alignment, use banded Smith-Waterman to create one. + +--- vaal-46233/src/pairwise_aligners/MatchList.cc ++++ vaal-46233/src/pairwise_aligners/MatchList.cc +@@ -9,6 +9,8 @@ + + #include "pairwise_aligners/MatchList.h" + ++using std::max; ++ + bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const + { + const vec<Match>& sortedMatches = m_sortedMatches[id1]; +--- vaal-46233/src/pairwise_aligners/SuffixTree.h ++++ vaal-46233/src/pairwise_aligners/SuffixTree.h +@@ -23,6 +23,8 @@ + #include <list> + #include <string> + ++using std::list; ++ + /** + * Implementation of a suffix tree for basevectors. + * This is a data structure for exact (sub)string matching. +--- vaal-46233/src/paths/AlignHyperKmerPath.cc ++++ vaal-46233/src/paths/AlignHyperKmerPath.cc +@@ -23,6 +23,9 @@ + #include "paths/KmerBaseBroker.h" + #include "paths/KmerPath.h" + ++using std::ostringstream; ++using std::set; ++ + // Function: AlignHyperKmerPath + // + // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed +--- vaal-46233/src/paths/AlignSeqsToHyper.cc ++++ vaal-46233/src/paths/AlignSeqsToHyper.cc +@@ -26,6 +26,7 @@ + #include "paths/ReadsToPathsCoreX.h" + #include "paths/SeqOnHyper.h" + ++using std::multimap; + + // Local class: simple_align + // +--- vaal-46233/src/paths/HyperKmerPath.cc ++++ vaal-46233/src/paths/HyperKmerPath.cc +@@ -19,6 +19,8 @@ + #include "paths/HyperKmerPath.h" + #include "paths/KmerBaseBroker.h" + ++using std::ostrstream; ++using std::ends; + + void HyperKmerPath::ReduceLoops( ) + { for ( int v = 0; v < N( ); v++ ) +--- vaal-46233/src/paths/KmerBaseBroker.h ++++ vaal-46233/src/paths/KmerBaseBroker.h +@@ -20,6 +20,8 @@ + #include <algorithm> // for set_union + #include <map> + ++using std::map; ++ + /** + Class: KmerBaseBrokerTemplate + +--- vaal-46233/src/paths/KmerPath.h ++++ vaal-46233/src/paths/KmerPath.h +@@ -22,6 +22,8 @@ + #include "HashSimple.h" + #include "graph/Digraph.h" + ++using std::make_pair; ++ + class KmerPathLoc; // forward declaration + + /** +--- vaal-46233/src/paths/KmerPathInterval.h ++++ vaal-46233/src/paths/KmerPathInterval.h +@@ -8,6 +8,8 @@ + #include "CommonSemanticTypes.h" + #include "feudal/BinaryStreamTraits.h" + ++using std::max; ++ + // Portability note: endianness + // The implementations here would need to be changed for big endian architectures. + +@@ -285,6 +287,12 @@ + Models <tagged read path interval>. + */ + // TODO: potentially dangerous truncation of index by PathId, ReadId ++template<class TAG> ++void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 ); ++ ++template<class TAG> ++void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 ); ++ + class tagged_rpint { + + public: /* PUBLIC METHODS */ +@@ -362,11 +370,11 @@ + + template<class TAG> + friend void Contains( const vec<TAG>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); +@@ -489,11 +497,11 @@ + + template<class TAG> + friend void Contains( const vec<TAG>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); +@@ -620,11 +628,11 @@ + + template<class TAG> + friend void Contains( const vec<TAG>& segs, kmer_id_t index, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, +- vec<longlong>& answer, bool append = false, int cap = -1 ); ++ vec<longlong>& answer, bool append, int cap ); + + template<class TAG> + friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k ); +--- vaal-46233/src/paths/ReadsToPathsCoreX.cc ++++ vaal-46233/src/paths/ReadsToPathsCoreX.cc +@@ -20,6 +20,8 @@ + #include "paths/MakeAlignsPathsParallelX.h" + #include "paths/ReadsToPathsCoreX.h" + ++using std::map; ++ + static inline + String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } + +--- vaal-46233/src/paths/SuperBaseVector.h ++++ vaal-46233/src/paths/SuperBaseVector.h +@@ -10,6 +10,8 @@ + #include <numeric> + #include <functional> + ++using std::mem_fun_ref; ++ + /// A simple class which holds a series of basevectors with + /// (possibly negative) gaps between them. This is what a + /// KmerPath logically maps to in sequence space. The function +--- vaal-46233/src/polymorphism/VAAL2.cc ++++ vaal-46233/src/polymorphism/VAAL2.cc +@@ -42,7 +42,7 @@ + #include "feudal/BinaryStream.h" + #include "feudal/VirtualMasterVec.h" + +-using namespace std; ++ + + // Trim reads so that they contain only kmers in the unipaths. + +--- vaal-46233/src/polymorphism/VAAL3.cc ++++ vaal-46233/src/polymorphism/VAAL3.cc +@@ -29,6 +29,8 @@ + #include "polymorphism/VAALTools.h" + #include "solexa/SolexaTools.h" + ++using std::ostringstream; ++ + int main( int argc, char *argv[] ) + { + RunTime( ); +--- vaal-46233/src/PrintAlignment.h ++++ vaal-46233/src/PrintAlignment.h +@@ -14,6 +14,8 @@ + #include "CoreTools.h" + #include "Qualvector.h" + ++using std::ostringstream; ++ + void PrintBlanks( ostream& out, int n ); + + template<class BASEVEC> +--- vaal-46233/src/Qualvector.cc ++++ vaal-46233/src/Qualvector.cc +@@ -10,6 +10,8 @@ + #include "FastIfstream.h" + #include "Qualvector.h" + ++using std::istrstream; ++ + /// \file + /// \ingroup grp_quals + /// \copydoc Qualvector.h +--- vaal-46233/src/SeqInterval.cc ++++ vaal-46233/src/SeqInterval.cc +@@ -9,6 +9,8 @@ + #include "SeqInterval.h" + #include "Vec.h" + ++using std::max; ++using std::min; + + /* + * seq_interval +--- vaal-46233/src/SeqInterval.h ++++ vaal-46233/src/SeqInterval.h +@@ -14,7 +14,9 @@ + #include <algorithm> + #include <iostream> + +-using namespace std; ++using std::binary_function; ++using std::ostream; ++using std::istream; + + /* + * class seq_interval +--- vaal-46233/src/Set.h ++++ vaal-46233/src/Set.h +@@ -16,7 +16,7 @@ + #include <set> + #include "CoreTools.h" + +-using namespace std; ++using std::set; + + template<class T> bool Member( const set<T>& the_set, const T& value ) + { return the_set.find(value) != the_set.end( ); } // Breaks cxx +--- vaal-46233/src/ShortVector.h ++++ vaal-46233/src/ShortVector.h +@@ -14,6 +14,8 @@ + #include "system/Types.h" + #include "feudal/BinaryStream.h" + ++using std::uninitialized_fill_n; ++ + // ================================================================================ + // + // A shortvector holds a list of up to 255 things of any type T. +--- vaal-46233/src/solexa/FourBase2.h ++++ vaal-46233/src/solexa/FourBase2.h +@@ -15,6 +15,10 @@ + #include "feudal/MasterVec.h" + #include "feudal/SerfVec.h" + ++using std::max_element; ++using std::min_element; ++using std::accumulate; ++ + class four_base2 { + + public: +--- vaal-46233/src/solexa/FourBase.cc ++++ vaal-46233/src/solexa/FourBase.cc +@@ -9,6 +9,9 @@ + + #include "solexa/FourBase.h" + ++using std::string; ++using std::istringstream; ++ + int four_base::Call( ) const + { + int result = 0; +--- vaal-46233/src/solexa/FourBase.h ++++ vaal-46233/src/solexa/FourBase.h +@@ -16,6 +16,8 @@ + #include "feudal/MasterVec.h" + #include "feudal/SerfVec.h" + ++using std::max; ++ + /* + Class: four_base + +--- vaal-46233/src/solexa/SolexaMetrics.h ++++ vaal-46233/src/solexa/SolexaMetrics.h +@@ -42,6 +42,8 @@ + #include "CommonSemanticTypes.h" + #include <map> + ++using std::map; ++ + /// Definition of general macros. + + class solexa_metric_db { +--- vaal-46233/src/solexa/SolexaTools.cc ++++ vaal-46233/src/solexa/SolexaTools.cc +@@ -20,6 +20,8 @@ + #include "FastaFileset.h" + #include "util/BaitMap.h" + ++using std::ostringstream; ++ + void SolexaPredictorParameters::SetFromFile(const String & fname) { + Ifstream(is, fname); + String params = Slurp(is); +--- vaal-46233/src/STLExtensions.h ++++ vaal-46233/src/STLExtensions.h +@@ -9,7 +9,7 @@ + #ifndef STLEXTENSIONS_H + #define STLEXTENSIONS_H + +-using namespace std; ++ + + #include <functional> + #include <vector> +@@ -21,6 +21,13 @@ + #include "feudal/BinaryStream.h" + #include "system/StaticAssert.h" + ++using std::binary_function; ++using std::unary_function; ++using std::pair; ++using std::bitset; ++using std::vector; ++using std::ostream; ++ + /// minimum<T> is a function object. + /// + /// If f is an object of class minimum<T> and x and y are objects of +--- vaal-46233/src/system/ParsedArgs.cc ++++ vaal-46233/src/system/ParsedArgs.cc +@@ -26,6 +26,9 @@ + #include "system/HostName.h" + #include "system/UseGDB.h" + ++using std::istrstream; ++using std::mem_fun_ref; ++ + #ifndef FatalErr + #define FatalErr(message) { cout << message << endl << endl; exit(-1); } + #endif +--- vaal-46233/src/system/ParsedArgs.h ++++ vaal-46233/src/system/ParsedArgs.h +@@ -97,6 +97,8 @@ + #include "TokenizeString.h" + #include "ParseSet.h" + ++using std::stringstream; ++ + class parsed_arg_help { + + public: +--- vaal-46233/src/system/ProcBuf.cc ++++ vaal-46233/src/system/ProcBuf.cc +@@ -15,6 +15,8 @@ + #include <sys/wait.h> + #include <unistd.h> + ++using std::ios_base; ++ + namespace + { + size_t const BUFFER_SIZE = 8192; +--- vaal-46233/src/system/RunTime.cc ++++ vaal-46233/src/system/RunTime.cc +@@ -41,6 +41,10 @@ + #include <unwind.h> + #endif + ++using std::strstream; ++using std::hex; ++using std::setw; ++ + /// =========================================================================== + /// + /// ReturnAddress(i), where 0 <= i <= 100: get the return address. The +--- vaal-46233/src/system/RunTime.h ++++ vaal-46233/src/system/RunTime.h +@@ -14,6 +14,8 @@ + #include "system/Exit.h" + #include "system/Types.h" + ++using std::ostream; ++ + typedef void ArachneSignalHandler(int, siginfo_t*, void*); + + void arachne_signal_handler( int signal_number, siginfo_t* info, void* context, +--- vaal-46233/src/system/System.cc ++++ vaal-46233/src/system/System.cc +@@ -35,6 +35,11 @@ + + #include <dirent.h> + ++using std::istringstream; ++using std::istream_iterator; ++using std::ostrstream; ++using std::ends; ++ + int SystemInternal( String command, const char *shell ) + { + flush(cout); +--- vaal-46233/src/system/System.h ++++ vaal-46233/src/system/System.h +@@ -21,6 +21,17 @@ + #include "system/Exit.h" + #include "system/file/TempFile.h" + ++using std::vector; ++using std::ostream; ++using std::ofstream; ++using std::cout; ++using std::flush; ++using std::endl; ++using std::istream; ++using std::ifstream; ++using std::ios; ++using std::setprecision; ++ + #ifndef InputErr + #define InputErr(message) \ + { cout << "\nFatal error at " << Date( ) << ": " << message << endl; \ +--- vaal-46233/src/system/TraceVal.h ++++ vaal-46233/src/system/TraceVal.h +@@ -24,6 +24,9 @@ + #include "system/Types.h" + #include "system/Assert.h" + ++using std::cout; ++using std::endl; ++ + // Macros: Tracing macros + // TRACEVAL_ON - undefine if you're not doing tracing + // TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles +--- vaal-46233/src/system/Types.h ++++ vaal-46233/src/system/Types.h +@@ -14,7 +14,7 @@ + #include <cstdlib> + #include <netinet/in.h> + +-using namespace std; ++ + + // This assumes that all suns run Solaris... + #if __sun == 1 +--- vaal-46233/src/util/BaitMap.cc ++++ vaal-46233/src/util/BaitMap.cc +@@ -236,7 +236,7 @@ + bool BaitMap::write(String file_name) + { + std::ofstream out(file_name.c_str()); +- ForceAssert(out); ++ ForceAssert(static_cast<bool>(out)); + + for (unsigned int i = 0; i < this->size(); i++) + { +@@ -250,7 +250,7 @@ + } + + out.close(); +- ForceAssert(out); ++ ForceAssert(static_cast<bool>(out)); + + return true; + } +@@ -260,7 +260,7 @@ + bool BaitMap::write_names(String file_name) + { + std::ofstream out(file_name.c_str()); +- ForceAssert(out); ++ ForceAssert(static_cast<bool>(out)); + + for (unsigned int i = 0; i < this->size(); i++) + { +@@ -268,7 +268,7 @@ + } + + out.close(); +- ForceAssert(out); ++ ForceAssert(static_cast<bool>(out)); + + return true; + } +--- vaal-46233/src/util/BaitMap.h ++++ vaal-46233/src/util/BaitMap.h +@@ -20,6 +20,8 @@ + + #include <map> + ++using std::map; ++ + class BaitMap + { + public: +--- vaal-46233/src/util/Qualb.cc ++++ vaal-46233/src/util/Qualb.cc +@@ -10,6 +10,8 @@ + #include "FastIfstream.h" + #include "Qualvector.h" + ++using std::istrstream; ++ + int main( int argc, char *argv[] ) + { + RunTime( ); +--- vaal-46233/src/Vec.h ++++ vaal-46233/src/Vec.h +@@ -48,6 +48,14 @@ + #include "Compare.h" + #include "system/file/FileReader.h" + ++using std::initializer_list; ++using std::numeric_limits; ++using std::ostream_iterator; ++using std::less; ++using std::equal_to; ++using std::setfill; ++using std::setw; ++ + ///////////////////////////////////////////////////////////////////////////// + // + // vec Class Declaration and Template Definitions +--- vaal-46233/src/VecUtilities.h ++++ vaal-46233/src/VecUtilities.h +@@ -37,6 +37,7 @@ + #include "Vec.h" + #include <cstddef> + ++using std::greater; + + ///////////////////////////////////////////////////////////////////////////// + // diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/vaal/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild new file mode 100644 index 000000000000..7185fc1c24df --- /dev/null +++ b/sci-biology/vaal/vaal-46233-r2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/" +SRC_URI=" + ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz + ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc" + +LICENSE="Whitehead-MIT" +SLOT="0" +KEYWORDS="amd64" +IUSE="openmp" + +RDEPEND=" + !sci-biology/allpaths + !sci-biology/allpathslg" +DEPEND=" + ${RDEPEND} + dev-libs/boost" + +DOCS=( "${DISTDIR}/VAAL_manual.doc" ) +PATCHES=( + "${FILESDIR}/${P}_remove-namespace-std.patch" +) + +src_prepare() { + sed \ + -e '/COPYING/d' \ + -i src/Makefile.am || die + + sed \ + -e 's:-ggdb::g' \ + -e '/AC_OPENMP_CEHCK/d' \ + -i configure.ac || die + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable openmp) +} diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest new file mode 100644 index 000000000000..d364d949bf1d --- /dev/null +++ b/sci-biology/vcftools/Manifest @@ -0,0 +1,6 @@ +AUX vcftools-0.1.14-buildsystem.patch 1159 SHA256 acb5156489d73a0b87785ad6717a781178844f3c063ba3c2b0b1a95fdc9cad7c SHA512 838cade29bbeeee090ea52f546c37b68eee868f3329ceccb710da0dbcf0f14e1b18dcc7b05ceefdbf72d400f450374389649f56fc6981bd86f6e176469b054ea WHIRLPOOL fa996b5909985075d00ae766bf070dbf15a214515aba56a0ac9f24a4f2116d94c6ae9b820d7f812bc6c75bf809f6b346276f04a49bc1ce0742e97db1889e8bdd +DIST vcftools-0.1.14.tar.gz 342369 SHA256 76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512 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b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch new file mode 100644 index 000000000000..126a709385db --- /dev/null +++ b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch @@ -0,0 +1,50 @@ +* Add prefix in Makefiles, not the configure script +* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB, + as it is more flexible and helps us with LAPACK +* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS + +--- a/configure.ac ++++ b/configure.ac +@@ -34,7 +34,7 @@ + [--with-pmdir=DIR], + [install Perl modules in DIR]), + [PMDIR=${withval}], +- [PMDIR='${prefix}'/"$pmdir_relative_path"]) ++ [PMDIR="$pmdir_relative_path"]) + + AC_SUBST([PMDIR]) + +@@ -73,9 +73,9 @@ + [pca=${enableval}], + [pca=no]) + +-if test "x${pca}" = "xyes" ; then +- AC_CHECK_LIB(lapack, dgeev_) +-fi ++AS_IF([test "x${pca}" = "xyes"],[ ++ AC_SEARCH_LIBS([dgeev_], [lapack]) ++]) + + # Generate output. + AC_CONFIG_FILES([Makefile +--- a/src/cpp/Makefile.am ++++ b/src/cpp/Makefile.am +@@ -1,6 +1,6 @@ + bin_PROGRAMS = vcftools + +-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS) ++vcftools_CPPFLAGS = $(ZLIB_CFLAGS) + vcftools_LDADD = $(ZLIB_LIBS) + + vcftools_SOURCES = \ +--- a/src/perl/Makefile.am ++++ b/src/perl/Makefile.am +@@ -24,7 +24,7 @@ + vcf-tstv \ + vcf-validator + +-pmdir = $(PMDIR) ++pmdir = $(exec_prefix)/$(PMDIR) + + dist_pm_DATA = \ + FaSlice.pm \ diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml new file mode 100644 index 000000000000..6c22d19200ae --- /dev/null +++ b/sci-biology/vcftools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">vcftools</remote-id> + <remote-id type="github">vcftools/vcftools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild new file mode 100644 index 000000000000..baa5f7c32ea5 --- /dev/null +++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools flag-o-matic perl-functions toolchain-funcs + +DESCRIPTION="Tools for working with VCF (Variant Call Format) files" +HOMEPAGE="http://vcftools.sourceforge.net/" +SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="lapack" + +RDEPEND="sys-libs/zlib + dev-lang/perl:= + lapack? ( virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + perl_set_version + + append-flags $($(tc-getPKG_CONFIG) --cflags lapack) + append-libs $($(tc-getPKG_CONFIG) --libs lapack) + + econf \ + $(use_enable lapack pca) \ + --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}" +} diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest new file mode 100644 index 000000000000..235f0e016e52 --- /dev/null +++ b/sci-biology/velvet/Manifest @@ -0,0 +1,8 @@ +AUX velvet-1.0.18-gentoo-r1.diff 7879 SHA256 5a177e3d0b027069aa44ce97d964ab7f8ab97561f00aa9c4485f110dafb6fa89 SHA512 7aa112850c1d83220e1545ef29aa3e445ce55bc4334d062c353a5c5681723a3492c8dec52aeb58cfb5d464d1c748b721dc6400509fa872a48c428a2e0f9cdbf0 WHIRLPOOL 2d1017fc91e9e8d9753f8d1a39af54c1ce4712ffb9932527d48c32d08e8ab8a82eba7dd767b3866935bbb0e2d2bf2af84a0e4d1cf3c15ea5ad42e1097d107dbc +DIST velvet_1.0.18.tgz 7598196 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad WHIRLPOOL 69dcb5a6760b66eba65d054562e873d2c000dc57b487cdcf2c977bc1c0106bf027a79ff3b7e81da8a0f82b00635b755c26135b34de51cae34f4d276f15c2be74 +DIST velvet_1.2.10.tgz 18818559 SHA256 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 WHIRLPOOL 595e40c92ab5724b3e9a5af11f023307da7c66628b0c96d2ac2c89617e2aaa8a84279252c397f52d4603119d6fcb4995d2bf6e38f7de8c7c9616bde3aefdcd64 +EBUILD velvet-1.0.18-r1.ebuild 1504 SHA256 1e15fb473ab7efd9e868a3e45189dd3f5c509f8b8658f98dc55d7a5801b3db76 SHA512 fe13e66f7d8eab941ba7fcd900967a13bd1f7279a63068275be1bdbcbd29aa29d6acf8b29ac8b9690936d8e95440c8eaec88c99a2da40270654dee2a29748ac0 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2011-01-27 17:01:45.088065521 +0000 +@@ -1,8 +1,4 @@ +-CC = gcc +-CFLAGS = -Wall +-DEBUG = -g +-LDFLAGS = -lm +-OPT = -O3 ++LIBS = -lm -lz + MAXKMERLENGTH=31 + CATEGORIES=2 + DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) +@@ -41,29 +37,29 @@ + -rm obj/*.o obj/dbg/*.o + + zlib : +- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o ++ echo "unbundled zlib" + + velveth : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(LIBS) + + + velvetg : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) + + debug : override DEF := $(DEF) -D DEBUG + debug : cleanobj obj/dbg +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) + + color : override DEF := $(DEF) -D COLOR + color : cleanobj obj_de +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) + + colordebug : override DEF := $(DEF) -D COLOR -D DEBUG + colordebug : cleanobj obj/dbg_de +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) + + objdir: + mkdir -p obj +@@ -83,7 +79,7 @@ + obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG) + + obj/%.o: src/%.c +- $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ ++ $(CC) $(CFLAGS) $(DEF) -c $? -o $@ + + obj/dbg/%.o: src/%.c + $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ +diff -durr src/readSet.c src/readSet.c +--- src/readSet.c 2011-01-27 16:52:58.804084948 +0000 ++++ src/readSet.c 2011-01-27 17:02:55.380324786 +0000 +@@ -24,6 +24,7 @@ + #include <math.h> + #include <time.h> + #include <limits.h> ++#include <zlib.h> + + #include "globals.h" + #include "tightString.h" diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/velvet/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild new file mode 100644 index 000000000000..4b7d1958cee6 --- /dev/null +++ b/sci-biology/velvet/velvet-1.0.18-r1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs flag-o-matic + +MY_P=${PN}_${PV} + +DESCRIPTION="A sequence assembler for very short reads" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/" +SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="-doc" +KEYWORDS="amd64 x86" + +RDEPEND="sys-libs/zlib" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + # necessary? + # append-flags -O3 # as recommended by upstream + epatch "${FILESDIR}"/${P}-gentoo-r1.diff + use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die +} + +src_compile() { + tc-export CC + MAKE_XOPTS="" + if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi + if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi + emake -j1 $MAKE_XOPTS || die + emake -j1 $MAKE_XOPTS color || die +} + +src_install() { + dobin velvet{g,h,g_de,h_de} || die + insinto /usr/share/${PN} + doins -r contrib || die + dodoc Manual.pdf CREDITS.txt ChangeLog || die +} + +pkg_postinst() { + elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual," + elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your" + elog "environment or /etc/portage/make.conf, then re-emerge the package. For example:" + elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet" +} diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild new file mode 100644 index 000000000000..d5a93f2f3e48 --- /dev/null +++ b/sci-biology/velvet/velvet-1.2.10.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +MY_P=${PN}_${PV} + +DESCRIPTION="A sequence assembler for very short reads" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/" +SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc openmp" + +RDEPEND="" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + if ! use doc; then + sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die + fi + elog "Upstream recommends using -O3 in CFLAGS" + echo + elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters" + elog "as described in the PDF manual, please set the variables by prepending VELVET_ in" + elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..." + elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge" + elog "the package. For example:" + elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet" + + if [[ $(tc-getCC) =~ gcc ]]; then + local eopenmp=-fopenmp + elif [[ $(tc-getCC) =~ icc ]]; then + local eopenmp=-openmp + else + elog "Cannot detect compiler type so not setting openmp support" + fi + append-flags -fPIC ${eopenmp} + append-ldflags ${eopenmp} + + tc-export CC + + MAKE_XOPTS=( + CC=$(tc-getCC) + CFLAGS="${CFLAGS}" + OPT="${CFLAGS}" + ) + use openmp && MAKE_XOPTS+=( OPENMP=1 ) + [[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ) + [[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ) + [[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} ) + [[ ! -z "${VELVET_LONGSEQUENCES}" ]] && MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} ) +} + +src_compile() { + emake "${MAKE_XOPTS[@]}" -j1 + emake "${MAKE_XOPTS[@]}" -j1 color +} + +src_test() { + emake "${MAKE_XOPTS[@]}" -j1 test +} + +src_install() { + dobin velvet{g,h,g_de,h_de} + insinto /usr/share/${PN} + doins -r contrib + dodoc Manual.pdf CREDITS.txt ChangeLog +} diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest new file mode 100644 index 000000000000..a1c0d2db95c5 --- /dev/null +++ b/sci-biology/vienna-rna/Manifest @@ -0,0 +1,12 @@ +AUX vienna-rna-2.1.1-bindir.patch 361 SHA256 cf5f393cb9ad1aba9e054d9ba7a0f876812ee88f2fa4d619ddc0b0ae2de3136a SHA512 f2e9da29f1ae3c1d3e7594367ef13ad0d44ebbcf1d9badf9d55c415e50b7e5af170dba7bcdad6438505786b941518f84ddb154cf1a6df60a229f3856cf333a94 WHIRLPOOL 5d28000ea19a6fbec28ff2a893ae77bc4ba0a70d74b5cb510a37d09563f278789379ee72e4aabc4facda873f6992ef707bd14732407547372174a1a4b9cccefc +AUX vienna-rna-2.1.1-impl-decl.patch 354 SHA256 9f9005092b060db501b51c37f215f9ca87da53720609ce971c3d9ad6bcf2ea39 SHA512 7c288b4889f11b5cc4e6db5b5db6dfcd70843aa135181e8d819ae86c90faed4a43e08f99b47f418caa23643642e68bf5e153f4d279f7566433af1c9093ec6e8b WHIRLPOOL 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3345b4e2f80c72ac38bb93cc4d12802dfcc2a0445847bf5b4e0858740aec95fdd13247796a85392ccb3fd47e4b5740b0b28233ae3d508435bfb14f3082583736 diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch new file mode 100644 index 000000000000..6d35ecea9b0f --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch new file mode 100644 index 000000000000..de457f318e8e --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch @@ -0,0 +1,15 @@ + Readseq/readseq.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/Readseq/readseq.c b/Readseq/readseq.c +index 8af7b39..56a25ae 100644 +--- a/Readseq/readseq.c ++++ b/Readseq/readseq.c +@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' + #include <stdio.h> + #include <string.h> + #include <ctype.h> ++#include <stdlib.h> + + #include "ureadseq.h" + diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch new file mode 100644 index 000000000000..ee4aef5c3308 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch @@ -0,0 +1,30 @@ + Readseq/Makefile | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Readseq/Makefile b/Readseq/Makefile +index f073aaa..05f2edd 100644 +--- a/Readseq/Makefile ++++ b/Readseq/Makefile +@@ -6,11 +6,11 @@ + # + + # pick an ANSI C compiler (the default Sun CC is not ANSI) +-CC=gcc # Gnu C Compiler ++CC?=gcc # Gnu C Compiler + #CC=cc # SGI Irix + #CC=vcc # some DEC Ultrix + +-CFLAGS= ++CFLAGS?= + #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum + # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software + +@@ -40,7 +40,7 @@ all: build test + + build: $(SOURCES) + @echo "Compiling readseq..." +- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c + + # if using NCBI, uncomment these lines in place of build: above + #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py new file mode 100644 index 000000000000..57f6b712ba3d --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py @@ -0,0 +1,27 @@ +from distutils.core import setup, Extension +import os +import sys + +old_filename = os.path.join("Perl", "RNA.py") +new_filename = os.path.join("Perl", "__init__.py") +if os.path.exists(old_filename): + os.rename(old_filename, new_filename) + +extra_link_args = [] + +extension = Extension("_RNA", + ["Perl/RNA_wrap.c"], + libraries=['RNA'], + library_dirs=['lib'], + extra_link_args=extra_link_args + ) + +setup(name="RNA", + version="2.1.1", + description="Vienna RNA", + author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", + url="http://www.tbi.univie.ac.at/RNA/", + package_dir = {'RNA':'Perl'}, + packages = ['RNA'], + ext_modules=[extension], + ) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch new file mode 100644 index 000000000000..e54dff95b485 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt ct2db + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml new file mode 100644 index 000000000000..861e9e38c31c --- /dev/null +++ b/sci-biology/vienna-rna/metadata.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> + The Vienna RNA Package consists of a C code library and several + stand-alone programs for the prediction and comparison of RNA secondary + structures. RNA secondary structure prediction through energy + minimization is the most used function in the package. We provide three + kinds of dynamic programming algorithms for structure prediction: the + minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a + single optimal structure, the partition function algorithm of + (McCaskill 1990) which calculates base pair probabilities in the + thermodynamic ensemble, and the suboptimal folding algorithm of + (Wuchty et.al 1999) which generates all suboptimal structures within a + given energy range of the optimal energy. For secondary structure + comparison, the package contains several measures of distance + (dissimilarities) using either string alignment or tree-editing + (Shapiro and Zhang 1990). Finally, we provide an algorithm to design + sequences with a predefined structure (inverse folding). +</longdescription> +</pkgmetadata> diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild new file mode 100644 index 000000000000..8b760b5a84bf --- /dev/null +++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild @@ -0,0 +1,111 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_OPTIONAL=true +AUTOTOOLS_AUTORECONF=true +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs + +DESCRIPTION="RNA secondary structure prediction and comparison" +HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" +SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz" + +SLOT="0" +LICENSE="vienna-rna" +KEYWORDS="amd64 ppc x86" +IUSE="doc openmp python static-libs" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-lang/perl + media-libs/gd + doc? ( dev-texlive/texlive-latex ) + python? ( ${PYTHON_DEPS} )" +DEPEND="${RDEPEND} + python? ( dev-lang/swig:0 )" + +S="${WORKDIR}/ViennaRNA-${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-bindir.patch + "${FILESDIR}"/${P}-prll.patch + "${FILESDIR}"/${P}-impl-decl.patch +) + +src_prepare() { + sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die + sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die + + autotools-utils_src_prepare + + if use python; then + cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die + PATCHES=() + distutils-r1_src_prepare + fi +} + +src_configure() { + local myeconfargs=( + --with-cluster + $(use_enable openmp) ) + + use doc || \ + myeconfargs+=( + --without-doc-pdf + --without-doc-html + --without-doc + ) + autotools-utils_src_configure + sed \ + -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \ + -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \ + -i RNAforester/g2-0.70/Makefile || die + sed \ + -e "s:CC=gcc:CC=$(tc-getCC):" \ + -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ + -i Readseq/Makefile || die + use python && distutils-r1_src_configure +} + +src_compile() { + autotools-utils_src_compile + autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) + + # TODO: Add (optional?) support for the NCBI toolkit. + if use python; then + pushd Perl > /dev/null + mv RNA_wrap.c{,-perl} || die + swig -python RNA.i || die + popd > /dev/null + distutils-r1_src_compile + mv Perl/RNA_wrap.c{-perl,} || die + fi +} + +src_test() { + autotools-utils_src_compile -C Perl check + autotools-utils_src_compile -C Readseq test +} + +src_install() { + autotools-utils_src_install + + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + fi + + newbin Readseq/readseq readseq-vienna + dodoc Readseq/Readseq.help + newdoc Readseq/Readme README.readseq + newdoc Readseq/Formats Formats.readseq + + # remove perlocal.pod to avoid file collisions (see #240358) + perl_delete_localpod || die "Failed to remove perlocal.pod" + use python && distutils-r1_src_install +} diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild new file mode 100644 index 000000000000..7664f6d3dc6e --- /dev/null +++ b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_OPTIONAL=true +AUTOTOOLS_AUTORECONF=true +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs + +DESCRIPTION="RNA secondary structure prediction and comparison" +HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" +SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz" + +SLOT="0" +LICENSE="vienna-rna" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="doc openmp python static-libs" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-lang/perl + media-libs/gd + doc? ( dev-texlive/texlive-latex ) + python? ( ${PYTHON_DEPS} )" +DEPEND="${RDEPEND} + python? ( dev-lang/swig:0 )" + +S="${WORKDIR}/ViennaRNA-${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-bindir.patch + "${FILESDIR}"/${PN}-2.1.1-prll.patch + "${FILESDIR}"/${PN}-2.1.1-impl-decl.patch +) + +src_prepare() { + sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die + sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die + + autotools-utils_src_prepare + + if use python; then + cd interfaces/Python || die + local PATCHES=() + distutils-r1_src_prepare + fi +} + +src_configure() { + local myeconfargs=( + --with-cluster + $(use_enable openmp) + ) + + use doc || \ + myeconfargs+=( + --without-doc-pdf + --without-doc-html + --without-doc + ) + autotools-utils_src_configure + sed \ + -e "s:CC=gcc:CC=$(tc-getCC):" \ + -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ + -i Readseq/Makefile || die + if use python; then + cd interfaces/Python || die + distutils-r1_src_configure + fi +} + +src_compile() { + autotools-utils_src_compile + autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) + + # TODO: Add (optional?) support for the NCBI toolkit. + if use python; then + cd interfaces/Python || die + emake RNA_wrap.c + distutils-r1_src_compile + fi +} + +src_test() { + autotools-utils_src_compile -C interfaces/Perl check + use python && autotools-utils_src_compile -C interfaces/Python check + autotools-utils_src_compile -C Readseq test +} + +src_install() { + autotools-utils_src_install + + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + fi + + newbin Readseq/readseq readseq-vienna + dodoc Readseq/Readseq.help + newdoc Readseq/Readme README.readseq + newdoc Readseq/Formats Formats.readseq + + # remove perlocal.pod to avoid file collisions (see #240358) + perl_delete_localpod || die "Failed to remove perlocal.pod" + if use python; then + cd interfaces/Python || die + distutils-r1_src_install + fi +} diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest new file mode 100644 index 000000000000..3767df9eb177 --- /dev/null +++ b/sci-biology/wgs-assembler/Manifest @@ -0,0 +1,6 @@ +AUX wgs-assembler-7.0-build.patch 10279 SHA256 23c0a916b3af24f4c12fd2c40f5e7c1559749ddf3d29f1f06c89dd27ff0fd462 SHA512 77e432319cb279d188ab74edda822f6b4dda127f1e5f1d75febb6fe0533b66d5bfd066781f1ff5d4d0d8f832c491d31ec470653b9c36b29d8280b5786783c5b9 WHIRLPOOL c964cc3b3b9394251b2701d8cdb8373184509a4ee62faa44cad5df11d0dff90ab03224d2538c888414cadeaac09a512128262e66791d3b4146c2d072d7f21052 +DIST wgs-7.0.tar.bz2 1952253 SHA256 fee425cf2ec6aec6e98d580cc7e43b53eb37abd7ca14e3edc1f953d2c09b3a6c SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba WHIRLPOOL a158b882e51e8ff80fa4e6bcbe4322125fce65fc64900407882a728de9465b778f59cc6d543142ca65a255295e66e89e5303774eeef7a66362c5f492ae99a92b +EBUILD wgs-assembler-7.0-r1.ebuild 1597 SHA256 6473cee0ef880fe8e7daf1809b0b018d20f954c0a77f9e534ae92da575cd0f3a SHA512 d874b917c4b86cfb56681473c4c99ec38bd9a681b7e0832a0e9240f2a1c20a754be30316ca4b64f579cbd8c3bb50cad18e874664f5e51e41194e6941088bcb86 WHIRLPOOL f257b4ff26490cab0e3e233438ca1cafb1be11204c0a38f28fea7ea8638928179a3ee97e18b6f71ffcfc4be5866ab5c3c4d79a3eb6c4cfefd555203f1802329e +MISC ChangeLog 2873 SHA256 1b44aed33035cb6bcaddfe9cf4f13bab73c82508e798f5703d8c57e2712912db SHA512 cfbe4601cce21311cd4a8343de00343506bf9168ca33042f86ef2626f6b411e0d2b9078a8fba2bc52137e8f3d0795f998a0c109d3974d0298fc0ff9095fc890b WHIRLPOOL 2b25fbf95083f85d51133edbffb4b869fec45a927fafa7e7beba3f1032909c136cdd3b9c0293cf52515ad7a7526d42bf61680be500e4d5ee7020690298428476 +MISC ChangeLog-2015 2127 SHA256 92fa1def396841cb4e895cc59a0a8351099efe39b3432ef034dae491bb4cd4ff SHA512 8dc7f0416773cf810ec1a5315045829322ba4887e2b0714965d8859cf1a847fa9fb37b7f5102aaec7b4e19f63f18df2ac50e8503aabb37287cce29f8f9ddfcd1 WHIRLPOOL 9429ff376104ae8b2e219a93fa99d6ec52b39e7994ca464dc7ae72e4d6ede9110168769b1a919591bce14d3c12864ec75da2da2415129d6aebc6effd2325680a +MISC metadata.xml 354 SHA256 e40bc21a4b4606897765d8a7e17d05d00513d64cf8b25294587150134d5e9b7b SHA512 b46f437eb224dbc7d7cec21941565ab48055f1d7b787fae7e66b135a8abeff0ea55dc191643d1e5f6212012001d98e4b7e8a7a655c9a66c9f3124bf7e700e193 WHIRLPOOL e654a2c11f819f97f8359a0cf8e57b651c45490146287954f84aaadad81a76be7fa08122b70442111c28111b6aa29a5986b3fc802ab048c9cc9ca9f955b688ea diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch new file mode 100644 index 000000000000..f7fb44743968 --- /dev/null +++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch @@ -0,0 +1,229 @@ + kmer/Make.rules | 4 ++-- + kmer/configure.sh | 20 +++++++++---------- + src/c_make.as | 58 +++++++++++++++++++++++++++---------------------------- + src/c_make.gen | 4 ++-- + 4 files changed, 43 insertions(+), 43 deletions(-) + +diff --git a/kmer/Make.rules b/kmer/Make.rules +index f904b13..5c2d477 100644 +--- a/kmer/Make.rules ++++ b/kmer/Make.rules +@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:% + ## EXE targets + ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}})) + ${ALL_C_EXES}: +- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS} ++ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS} + __SUBGOALS__+=$${${1:.=.C_EXES}} + + ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) + ${ALL_CXX_EXES}: +- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} ++ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} + __SUBGOALS__+=$${${1:.=.CXX_EXES}} + + define .RULE-install-copy-C-CXX-EXES +diff --git a/kmer/configure.sh b/kmer/configure.sh +index 2f0d5ea..9daf89f 100755 +--- a/kmer/configure.sh ++++ b/kmer/configure.sh +@@ -254,13 +254,13 @@ EOF + # -*- makefile -*- + # Linux, optimized + CC := $CC +-SHLIB_FLAGS := -shared +-CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CLDFLAGS := -L/usr/local/lib ++SHLIB_FLAGS := -shared ${LDFLAGS} ++CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CLDFLAGS := + CLIBS := -pthread -ldl + CXX := $CXX +-CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CXXLDFLAGS := -L/usr/local/lib ++CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CXXLDFLAGS := + CXXLIBS := -pthread -ldl + ARFLAGS := ruvs + INSTALL/ := $target/ +@@ -272,13 +272,13 @@ EOF + # -*- makefile -*- + # Linux64, optimized + CC := $CC +-SHLIB_FLAGS := -shared +-CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CLDFLAGS := -L/usr/local/lib ++SHLIB_FLAGS := -shared ${LDFLAGS} ++CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CLDFLAGS := + CLIBS := -pthread -ldl + CXX := $CXX +-CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CXXLDFLAGS := -L/usr/local/lib ++CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CXXLDFLAGS := + CXXLIBS := -pthread -ldl + ARFLAGS := ruvs + INSTALL/ := $target/ +diff --git a/src/c_make.as b/src/c_make.as +index 0172807..4304589 100644 +--- a/src/c_make.as ++++ b/src/c_make.as +@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen + + ifeq ($(OSTYPE), Linux) + ifeq ($(MACHINETYPE), i686) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX + ARCH_LIB = /usr/X11R6/lib + endif + ifeq ($(MACHINETYPE), amd64) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX + ARCH_LIB = /usr/lib64 /usr/X11R6/lib64 + endif + ifeq ($(MACHINETYPE), ia64) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 + ARCH_LIB = /usr/X11R6/lib + endif + + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -g +- ARCH_LDFLAGS += ++ ARCH_CFLAGS += ++ LINK_LIBS += + else +- ARCH_CFLAGS += -O2 +- ARCH_LDFLAGS += -Wl,-O1 ++ ARCH_CFLAGS += ++ LINK_LIBS += + endif + endif + +@@ -94,19 +94,19 @@ endif + + ifeq ($(OSTYPE), FreeBSD) + ifeq ($(MACHINETYPE), i386) +- ARCH_LDFLAGS += -pthread -lthr -lm +- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare +- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare ++ LINK_LIBS += -pthread -lthr -lm ++ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare ++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare + endif + ifeq ($(MACHINETYPE), amd64) +- ARCH_LDFLAGS += -pthread -lthr -lm +- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat +- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat ++ LINK_LIBS += -pthread -lthr -lm ++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat ++ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat + endif + + ifeq ($(BUILDCOVERAGE), 1) + ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage +- ARCH_LDFLAGS += -lgcov ++ LINK_LIBS += -lgcov + else + ifeq ($(BUILDDEBUG), 1) + ARCH_CFLAGS += -g +@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin) + + ifeq ($(MACHINETYPE), i386) + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g +- ARCH_LDFLAGS += -m64 -lm ++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g ++ LINK_LIBS += -m64 -lm + else + # Wow, -Wshorten-64-to-32 is tough +- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast ++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast + # ARCH_CFLAGS += -Wextra + # ARCH_CFLAGS += -pedantic (see above about pedantic) +- ARCH_LDFLAGS += -m64 -lm ++ LINK_LIBS += -m64 -lm + endif + endif + +@@ -161,23 +161,23 @@ endif + ifeq ($(OSTYPE), SunOS) + ifeq ($(MACHINETYPE), i86pc) + ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -lm ++ LINK_LIBS += -lm + endif + + ifeq ($(MACHINETYPE), sparc32) + ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -lm -lnsl -lsocket ++ LINK_LIBS += -lm -lnsl -lsocket + endif + + ifeq ($(MACHINETYPE), sparc64) + ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket ++ LINK_LIBS += -lm -lnsl -lsocket + endif + + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -g ++ ARCH_CFLAGS += + else +- ARCH_CFLAGS += -O ++ ARCH_CFLAGS += + endif + endif + +@@ -186,14 +186,14 @@ endif + + ifeq ($(BUILDPROFILE), 1) + ARCH_CFLAGS += -pg +- ARCH_LDFLAGS += -pg ++ LINK_LIBS += -pg + endif + + # One can argue that CXXFLAGS should be separate. For now, we only + # add to the flags. + + CFLAGS += $(ARCH_CFLAGS) +-CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS) ++CXXFLAGS += $(ARCH_CXXFLAGS) + LDFLAGS += $(ARCH_LDFLAGS) + + INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) +@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB) + OBJ_SEARCH_PATH = $(LOCAL_OBJ) + + ifeq ($(SITE_NAME), JCVI) +- LDFLAGS += -lcurl ++ LINK_LIBS += -lcurl + endif + + # The order of compilation here is very carefully chosen to be the +diff --git a/src/c_make.gen b/src/c_make.gen +index 7b5227c..c27b777 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -396,12 +396,12 @@ $(LIBRARIES): + $(C_PROGS): + @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; + cd $(LOCAL_OBJ); \ +- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) + + $(CXX_PROGS): + @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; + cd $(LOCAL_OBJ); \ +- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) + + $(SCRIPT_PROGS): %.sh: + @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml new file mode 100644 index 000000000000..fa8a259ff764 --- /dev/null +++ b/sci-biology/wgs-assembler/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">wgs-assembler</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild new file mode 100644 index 000000000000..066654dcfb92 --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" +HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/" +SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="static-libs" + +DEPEND=" + x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_configure() { + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install + emake -C src -j1 SITE_NAME=LOCAL +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/${MY_S}/bin/* + insinto /usr/$(get_libdir)/${PN} + use static-libs && doins kmer/${MY_S}/lib/* + + insinto /usr/include/${PN} + doins kmer/${MY_S}/include/* + + insinto /usr/share/${PN}/lib + doins -r ${MY_S}/bin/TIGR + rm -rf ${MY_S}/bin/TIGR || die + dobin ${MY_S}/bin/* + use static-libs && dolib.a ${MY_S}/lib/* + dodoc README +} diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest new file mode 100644 index 000000000000..e3d179c6a9f9 --- /dev/null +++ b/sci-biology/wise/Manifest @@ -0,0 +1,9 @@ +AUX wise-2.4.0_alpha-cflags.patch 27241 SHA256 281c95e7f37f217a9bd730ba4d80640a6085dc134fb3dcd837f217b36f5b5b87 SHA512 2f4faaff8198c63fb22edde934584fa2d00d2a333c5caefbbbc569e6136546aa274060453f093e0791a4d61bc901e1f199c47bb60d1be9f0ac32b3709cb025ab WHIRLPOOL 2b48020dde9e0f19a3ff32f2db6d0d08ea5626e0f11eb8560c23160ae716fa55ac3a2946bcfb6e90c018db98df7ee38eb66f44acef6828d29f67d00fbd9f58d6 +AUX wise-2.4.0_alpha-glibc-2.10.patch 8068 SHA256 caaacdde33b1f0b12aa0854fa27e3b2c4d6bab099dbc627e18057609763ce265 SHA512 eba50ed8e12ca94d026fed95602ec1d1683ea26f0195952304a1caebdb94df700b547168a6da4a9ad4289dd9c6060572b4ed9dcfcc7698dff2812765adc556e1 WHIRLPOOL 38228826603523ab1d5d31b02e57016e128788d3767820f6a2efb79234f01e6ffec63480430c5ec7cf21ea24351aece8ad0303ea7ec0aacfa4868989bb4a82dd +AUX wise-api.tex.patch 2234 SHA256 31042f660669ea9df9bc608006cd40479e004f5cbb9aed055d3ec58a853c145d SHA512 1cb7b5f5377d4d235707d32d74087598db5abc793b2aba8272a7da941a25d5618691212240eb25c078df39868ea7adfacfba3d218bd77fcea5d57b3b2ef51a0b WHIRLPOOL 523d0b0fa7c97669ca1e4e2229bb432ebe1002d7d0249064217591b0c542d4fc6171e5e924bd650c71d46e02d4c180b2763d1b1f1d87b077a55cbf1e53e3c6ac +AUX wise-env 40 SHA256 de6f742147c43b3820ea261fd158647ae1d2d9e8fe562e0b5c4c0d7e878ced36 SHA512 58cfa40d4d3b2623df82bb321f8dd2f5ebbee099ccfd4ac0e3eb9edf5693dbaee0581f8986b4923c60060d92c028e731f15c047e18f86efb76adaf4ec386e96c WHIRLPOOL 62228e902a0b962ad13514b76a2fe52eb3d6626c7536d63c3425c1e11abed08f4c9e971b7d30b78950e3ba0fbf5e020cd6286148419692f5c6d93876e0e6a8eb +DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec +EBUILD wise-2.4.0_alpha.ebuild 1629 SHA256 9121d9c9acb7ea103e742070a9f22985e403fe28b688ec9335cabe678a7f0a7f SHA512 cf1b57b1d14396ed4da12a1f24932a6a6e43a5e4eb61642bc40906eea4dbc57c58c0c4daac29122744b8c54b5f434e5f49d964d3fbc05b60dac6cd02514f2f43 WHIRLPOOL 74e6990628fd9935a8399ff16dc64bee300e4873e77fb8525fdc360d207269e2811d4927e2cdda49fc1cd135a09cc00c6a49b6a532b2b441cf5025b51e2d0e96 +MISC ChangeLog 2597 SHA256 482a2dc882cc4a7b5fef4dd2bd14004ace6c42181c95a33246254f8f679581fa SHA512 725a0ee890e65febdcff9b5b2f5d8b298988633efa472b10dd3918cc6fa0b8ea2237b8bad7fa15409a1accd28d861e272aa67480f8ba2b8a2d6c90fa915713d9 WHIRLPOOL 2cd895b442a4f6009a48283819958fb985768e901094ea826821050a39fad2711c45f5c82daef709e9b69c238a80b840cac976f438388cc5a0e3e32c80334c84 +MISC ChangeLog-2015 2958 SHA256 89da20b9ff628f1582a29544932a00af4f071b41d49c6dcc12fae19465544ac2 SHA512 6342c0e4b676dca1698bae42a470d0f931528791cb6a77b239609c74986b2e80574e6372308d1aef91bb23221d7719a052079bb51b5196c24f90fa89cb75141f WHIRLPOOL 9e22b0b177da5773f6f0be267ea8642c64ac49c0be1167a7896054866ec5d596f879b915229fefd6a934e636629ce7a145b3995758bb9635e3814af7ed2449e1 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch new file mode 100644 index 000000000000..d3c17098105e --- /dev/null +++ b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch @@ -0,0 +1,407 @@ +diff --git a/src/base/makefile b/src/base/makefile +index 4620f19..a84e2c7 100644 +--- a/src/base/makefile ++++ b/src/base/makefile +@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \ + + + #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++CFLAGS += -c -DUNIX -pthread ++LFLAGS = -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +diff --git a/src/corba/makefile b/src/corba/makefile +index df3dd78..237a1ba 100644 +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -1,10 +1,10 @@ + + +-CC = cc ++CC += gcc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/ ++CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags` + LFLAGS = -L../base/ -lm -lpthread + AR_OPTIONS = ru + +@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile +index ef3334a..3a0bc2a 100644 +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm + + + .c.o : +diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile +index 285e6a0..8c6a0dc 100644 +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + make_shotgun : make_shotgun.o shotgun.o + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) +@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm + + + .c.o : +diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile +index d1d77af..cad8900 100644 +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \ + + + +-CC = cc ++CC ?= gcc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` ++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ + LFLAGS = -g -L../base/ -lm + AR_OPTIONS = ru +@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a + $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +diff --git a/src/external/mott/makefile b/src/external/mott/makefile +index 8d7c1d4..940c438 100644 +--- a/src/external/mott/makefile ++++ b/src/external/mott/makefile +@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o + wise2_mott_bridge.o : wise2_mott_bridge.c + $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c + +-CC = cc ++CC ?= gcc + +-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c +-LFLAGS = -g -L../base/ -lm ++CFLAGS += -DPTHREAD -c ++LFLAGS = -L../base/ -lm + AR_OPTIONS = ru + + +diff --git a/src/makefile b/src/makefile +index bdff4ff..0d7c871 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -26,12 +26,12 @@ + + # Change the cc line to gcc if you get compiler errors + # Most likely you have a non ANSI C compiler +-CC ?= cc ++CC ?= gcc + + # These are the CFLAGS to use. These days Wise2 is inherently + # pthreaded, and everything is compiled with threads. More + # info on running threads can be found in the documentation +-CFLAGS = -c -pthread -O2 `glib-config --cflags` ++CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags` + + + +diff --git a/src/models/makefile b/src/models/makefile +index f518d0c..a297eff 100644 +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -50,6 +50,8 @@ NEWG = geneparser21.o \ + proteinsw.o \ + estquick3.o + ++EXTRALIBS += `pkg-config glib-2.0 --libs` ++ + all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a + + libmodel.a : $(NEWG) +@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm ++ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm + + testdna : testdna.o dnaalign.o seqaligndisplay.o + $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) +@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c +@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc. + + + scanwisep_wiseserver.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` + + scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs` + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap. + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread +@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o + $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm ++ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence ++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence ++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +347,11 @@ HMMER_DEFINE = + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` ++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` + #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +diff --git a/src/network/makefile b/src/network/makefile +index 303c2da..e607310 100644 +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags` ++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +diff --git a/src/snp/makefile b/src/snp/makefile +index ccf750a..2b83c43 100644 +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -2,12 +2,12 @@ + .SUFFIXES : .dy + + +-CC = cc ++CC ?= gcc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0 + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch new file mode 100644 index 000000000000..42af0c7e849b --- /dev/null +++ b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch @@ -0,0 +1,302 @@ +diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c +index 5889e7d..bc95629 100644 +--- a/src/HMMer2/sqio.c ++++ b/src/HMMer2/sqio.c +@@ -213,7 +213,7 @@ readline(FILE *f, char *s) + } + } + +-/* Function: getline() ++/* Function: get_line() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ readline(FILE *f, char *s) + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V) + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V) + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V) + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V) + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V) + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V) + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V) + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V) + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V) + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V) + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V) + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V) + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) get_line(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V) + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V) + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V) + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V) + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V) + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V) + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V) + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V) + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V) + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V) + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env) + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset) + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp) + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch new file mode 100644 index 000000000000..827ce4cdfa7a --- /dev/null +++ b/sci-biology/wise/files/wise-api.tex.patch @@ -0,0 +1,38 @@ +--- api.tex.old 2005-03-06 11:31:59.862760952 -0500 ++++ api.tex 2005-03-06 11:42:31.375756384 -0500 +@@ -204,7 +204,7 @@ + \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) + \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins + \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) +-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) ++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) + \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) + \end{itemize} + +@@ -213,7 +213,7 @@ + \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) + \item Make a protein database from the single protein object (\ref{object_ProteinDB}) + \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) +-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) ++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) + \item Show the Hscore object using a show function (\ref{object_Hscore}) + \item Retrieve individual protein objects from the database by taking out the + DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object +@@ -232,7 +232,7 @@ + \item Read in a codon table (\ref{object_CodonTable}) + \item Make a random DNA model (\ref{object_RandomModelDNA}) + \item Make an algorithm type (\ref{module_gwrap}) +-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) ++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) + \item Run the actual algorithm (\ref{module_gwrap}) + \item show the alignment using genedisplay (\ref{module_gwrap}) + \end{itemize} +@@ -5055,7 +5055,7 @@ + Member functions of RandomModel + + \section{sequence\_codon} +-\label{module_sequence\_codon} ++\label{module_sequence_codon} + This module only contains factory methods + + \subsection{sequence\_codon factory methods} diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env new file mode 100644 index 000000000000..3f781c80833b --- /dev/null +++ b/sci-biology/wise/files/wise-env @@ -0,0 +1 @@ +WISECONFIGDIR="/usr/share/wise/wisecfg" diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/wise/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild new file mode 100644 index 000000000000..3d4f0955d848 --- /dev/null +++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +DESCRIPTION="Intelligent algorithms for DNA searches" +HOMEPAGE="http://www.ebi.ac.uk/Wise2/" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc static-libs" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND=" + ${RDEPEND} + app-shells/tcsh + dev-lang/perl + virtual/latex-base" + +S="${WORKDIR}"/${PN}$(delete_version_separator 3) + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-glibc-2.10.patch \ + "${FILESDIR}"/${P}-cflags.patch + cd "${S}"/docs || die + cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die + cat wise2api.tex temp.tex apiend.tex > api.tex || die + epatch "${FILESDIR}"/${PN}-api.tex.patch +} + +src_compile() { + emake \ + -C src \ + CC="$(tc-getCC)" \ + all + if use doc; then + cd "${S}"/docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd "${S}"/src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb + use static-libs && \ + dolib.a \ + "${S}"/src/base/libwisebase.a \ + "${S}"/src/dynlibsrc/libdyna.a \ + "${S}"/src/models/libmodel.a + + insinto /usr/share/${PN} + doins -r "${S}"/wisecfg + + if use doc; then + insinto /usr/share/doc/${PF} + doins "${S}"/docs/*.ps + fi + newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" +} diff --git a/sci-biology/yass/Manifest b/sci-biology/yass/Manifest new file mode 100644 index 000000000000..fed19b131f6d --- /dev/null +++ b/sci-biology/yass/Manifest @@ -0,0 +1,6 @@ +AUX 1.14-as-needed.patch 6046 SHA256 16a8e8e042ef6af33b49145fca2da1f4c1dae4f5fcd692509eda8d867cbb8ecd SHA512 4b9227bb16556084121336b01d6d02257ccf7e35765db53b4a6ba2b0a41946a6b600a9dd05156b763b4b37f18d30d2c9111eeca79a1656f757199ba1cda5b3dd WHIRLPOOL 5c4ad2c59472ed93df27c4e9a8d5d29cb9c9e7b84b6318b2e21a799c671cc5b9f7f27408148ac79065f89b5d2fe2957dd7db55f30d01c1f0615a315d3a5cfc2c +DIST yass-1.14.tar.gz 235530 SHA256 f23da1c16cf98317ad11c085feede9790401e888a95d486b550f0c081d4c9018 SHA512 fdfac6f391848d0bd35829a966721a242697b0832803092bd7ea2116149332642ddf3bf5f095fe707f6edbbb9454efe068852fe6d5cdfe937445d9d32a521fa2 WHIRLPOOL e5aabfabe7a1b001e5b41c2fd17dfc345ae66ba06d42decaacfd7948fc60aa38d90ca9d2d7a05cb0d7fa3216dbf125ec64d2341ee4e9c1ffa91b69f60e8a3728 +EBUILD yass-1.14-r2.ebuild 663 SHA256 34ba5ddb35fe3ce8bcc7bfa78a4eb156c57911214d797d30c769c622acc8bdbe SHA512 ac373f6d89d678ca71d0e84d76965cc2d3eed9ccf51d33c799613bcdb588f5adfc7ca588b823a92ea6bb12c39bb91fca6cdd685af3a8ec943a43192b633246cc WHIRLPOOL e1ff4e60a01bdcf1df0684b2ca1596853a0009fe48532a8c3b07f5e9a04670951eb36b02bab0afb0103a97d59fd57826c9741b63f4c6d340d9f31063d2c9ce1c +MISC ChangeLog 2808 SHA256 36408d37a9418e7618211341f457a4dce25fc9f0ca711db9862d215e855a6519 SHA512 46095a17fa40a05dc57a00c78b1d326dd55dc8620ddcf340f2dbbedad22aa561c68726241aeb5096b6c67f42fdef91707ef4569565de25c87732b1559c62074d WHIRLPOOL de75615af31a0051077809b0d56d1b02174b1ec40b72b61e373fed913e4c65cc9bba1810e0ea43c1832c1526b431202e821771ee6eb14a5ea573701a6da8e7b7 +MISC ChangeLog-2015 675 SHA256 ae16ce2beb0da9bd6036d65853da5d15e0b357d5d351dd871aea5f4eec0f4265 SHA512 13ae8cfa681e40ee21cf3dca9f47ebcf7bf0dc14b4c446cd503e5be9bfeb70e87b701d15ff86b7f2603f5ff0233e1354910399d5baaeead597ed6d5074cebea9 WHIRLPOOL efd335d71098594ebfe42a080d923111c3acd3c861db0e5dc6331cbc2eac4cd36a7b504de5babbced9349428f3a895810a6c0299b317e3a76e7b9dc384b191a7 +MISC metadata.xml 439 SHA256 9d66ed15ddabe6d56a5a820c57b95fc4cb91f1b4ac9a3a0221072e04d077693b SHA512 e2f368f4a1b1b46ee31e1308c9a57846b08d9a4958a53caed2f2a9c8f228459cf305e1d07ac4f294bd6eca622094a36be0ec2859f86bd9eecf10070ea832d7af WHIRLPOOL 7747dec3f247172eaddc2e58e24a179e74708a9c7340d9dfc917e9f16be3cf9df66b130e6f385c62f06d9b4d5c9ddab597957053c9de7a6ecc97d28148ca8c13 diff --git a/sci-biology/yass/files/1.14-as-needed.patch b/sci-biology/yass/files/1.14-as-needed.patch new file mode 100644 index 000000000000..e57503801c7a --- /dev/null +++ b/sci-biology/yass/files/1.14-as-needed.patch @@ -0,0 +1,207 @@ +diff --git a/configure.ac b/configure.ac +index 68453ef..3ecfd21 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul]) + dnl 1) threads options + + dnl abc) : with-threads option +-AC_ARG_WITH( +- threads, +- [ --with-threads compile with all threads], +- [threads="yes"], +- [threads="no"]) ++AC_ARG_ENABLE( ++ [threads], ++ AS_HELP_STRING([--enable-threads], [compile with all threads])) + +-if test "$threads" = "yes"; then ++AS_IF([test "x$enable_threads" = "xyes"], [ + AC_MSG_RESULT(detected cpu parameter: threads); + + dnl pthread library here ? (UNIX system) +@@ -46,167 +44,25 @@ if test "$threads" = "yes"; then + AC_MSG_RESULT(yes) + AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) + CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK " +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + else + AC_MSG_RESULT(no : disabling \"--with-threads\" parameter) + fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-threads\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +- +- +- +-dnl a) : with-thread-fr option +-AC_ARG_WITH( +- thread-fr, +- [ --with-thread-fr compile with two separate threads for Forward and Reverse sequence], +- [thread_forward_reverse="yes"], +- [thread_forward_reverse="no"]) +- +-if test "$thread_forward_reverse" = "yes"; then +- AC_MSG_RESULT(detected cpu parameter: thread-fr); +- +- dnl pthread library here ? (UNIX system) +- AC_MSG_CHECKING(for pthread lib) +- AC_CHECK_LIB(pthread, pthread_create, +- [have_pthread="yes"], +- [have_pthread="no"]) +- if test "$have_pthread" = "yes"; then +- AC_MSG_RESULT(yes) +- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) +- CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE " +- LDFLAGS="$LDFLAGS -lpthread" +- else +- AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter) +- fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-thread-fr\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +- +- +- +-dnl b) : with-thread-aa option +-AC_ARG_WITH( +- thread-aa, +- [ --with-thread-aa compile with two separate threads for Assemble and Align steps], +- [thread_assemble_align="yes"], +- [thread_assemble_align="no"]) +- +-if test "$thread_assemble_align" = "yes"; then +- AC_MSG_RESULT(detected cpu parameter: thread-aa); +- +- dnl pthread library here ? (UNIX system) +- AC_MSG_CHECKING(for pthread lib) +- AC_CHECK_LIB(pthread, pthread_create, +- [have_pthread="yes"], +- [have_pthread="no"]) +- if test "$have_pthread" = "yes"; then +- AC_MSG_RESULT(yes) +- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) +- CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN " +- LDFLAGS="$LDFLAGS -lpthread" +- else +- AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter) +- fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-thread-aa\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +-dnl c) : with-thread-qc option +-AC_ARG_WITH( +- thread-qc, +- [ --with-thread-qc compile with threads for the query chunks], +- [thread_query_chunk="yes"], +- [thread_query_chunk="no"]) +- +-if test "$thread_query_chunk" = "yes"; then +- AC_MSG_RESULT(detected cpu parameter: thread-qc); +- +- dnl pthread library here ? (UNIX system) +- AC_MSG_CHECKING(for pthread lib) +- AC_CHECK_LIB(pthread, pthread_create, +- [have_pthread="yes"], +- [have_pthread="no"]) +- if test "$have_pthread" = "yes"; then +- AC_MSG_RESULT(yes) +- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) +- CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK " +- LDFLAGS="$LDFLAGS -lpthread" +- else +- AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter) +- fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-thread-qc\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +- ++]) + + dnl 2) : low-memory option +-AC_ARG_WITH( +- low-memory, +- [ --with-low-memory use less memory, but can miss some repeats], +- [low_memory="yes"], +- [low_memory="no"]) ++AC_ARG_ENABLE( ++ [lowmemory], ++ AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats])) + +-if test "$low_memory" = "yes"; then ++AS_IF([test "x$enable_lowmemory" = "xyes"], [ + AC_MSG_RESULT(detected memory parameter: low memory); + CFLAGS=" $CFLAGS -DLOW_MEMORY " +-else +- AC_MSG_RESULT(detected memory parameter : plain memory) +-fi +- +- +-CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer " +-LDFLAGS="$LDFLAGS -lm" ++]) + + AC_SUBST(CFLAGS) + AC_SUBST(LDFLAGS) ++ + AM_WITH_DMALLOC + AM_INIT_AUTOMAKE + AC_CONFIG_FILES([Makefile +diff --git a/src/Makefile.am b/src/Makefile.am +index e456f94..8d90ca9 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -6,3 +6,4 @@ + bin_PROGRAMS = yass + yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \ + align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h ++yass_LDADD = -lm diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml new file mode 100644 index 000000000000..67dfef524416 --- /dev/null +++ b/sci-biology/yass/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="dmalloc">Enable debugging with the dmalloc library</flag> + <flag name="lowmem">Build for environments with low amounts of memory</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/yass/yass-1.14-r2.ebuild b/sci-biology/yass/yass-1.14-r2.ebuild new file mode 100644 index 000000000000..cdbe54f0bef6 --- /dev/null +++ b/sci-biology/yass/yass-1.14-r2.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds" +HOMEPAGE="http://bioinfo.lifl.fr/yass/" +SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="dmalloc lowmem threads" +KEYWORDS="~amd64 ~x86" + +DEPEND="dmalloc? ( dev-libs/dmalloc )" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable threads) \ + $(use_enable lowmem lowmemory) \ + $(use_with dmalloc) +} |