From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/GBrowse/GBrowse-2.48-r1.ebuild | 71 +++++++++++++++++++++ sci-biology/GBrowse/Manifest | 6 ++ .../GBrowse/files/GBrowseInstall.pm-2.39.patch | 72 ++++++++++++++++++++++ sci-biology/GBrowse/metadata.xml | 11 ++++ 4 files changed, 160 insertions(+) create mode 100644 sci-biology/GBrowse/GBrowse-2.48-r1.ebuild create mode 100644 sci-biology/GBrowse/Manifest create mode 100644 sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch create mode 100644 sci-biology/GBrowse/metadata.xml (limited to 'sci-biology/GBrowse') 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/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 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + GBrowse + + -- cgit v1.2.3