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/embassy-hmmer/Manifest | 7 ++ .../embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild | 21 +++++ .../embassy-hmmer-2.3.2.650_fix-build-system.patch | 100 ++++++++++++++++++++ .../embassy-hmmer-2.3.2.660-slotted-hmmer2.patch | 101 +++++++++++++++++++++ sci-biology/embassy-hmmer/metadata.xml | 11 +++ 5 files changed, 240 insertions(+) create mode 100644 sci-biology/embassy-hmmer/Manifest create mode 100644 sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild create mode 100644 sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch create mode 100644 sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch create mode 100644 sci-biology/embassy-hmmer/metadata.xml (limited to 'sci-biology/embassy-hmmer') 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 7e1894fc952af1ffca66785790c94851b1dbdb6bb9530f18abef2862adbde171a731ab4d61f60dc2add66a7638dde778a3effc078047b8d9a39e70be2686b0c7 +DIST embassy-hmmer-2.3.2.660.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83 +EBUILD embassy-hmmer-2.3.2.660.ebuild 501 SHA256 7750aa84f23f0fb4748984397ae166c2677ab167749526bf26ff0e21f7c548b1 SHA512 bee21c5e7950f2f11be84c0287010630754681d840fc7393f9fc8e0c05fd14169e03f37a6d99bc4dfb28dae5b9f78a9f509a163cee6722796a3300b0cdab0651 WHIRLPOOL e2682a83bfa88731f25b9789a181e0c3c4207b183f1c4f73e16ba26a2a95395fc780c3149d46541eed1b2991ed553b44ba6bd71bbd807b6d6c00c1afd3bba5f7 +MISC ChangeLog 3694 SHA256 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 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + emboss + + -- cgit v1.2.3