commit: 5d1cf37ff6399cd2ad05dd51f23f67a24f94ae2e Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Apr 30 09:25:42 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Apr 30 09:25:42 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d1cf37f
sci-biology/trinityrnaseq: new package (with last release on sourceforge) Package-Manager: portage-2.2.18 sci-biology/trinityrnaseq/ChangeLog | 10 +++++ sci-biology/trinityrnaseq/files/r3590_chmod.patch | 24 +++++++++++ sci-biology/trinityrnaseq/files/sort.patch | 14 +++++++ sci-biology/trinityrnaseq/metadata.xml | 9 ++++ .../trinityrnaseq/trinityrnaseq-20140413.ebuild | 49 ++++++++++++++++++++++ 5 files changed, 106 insertions(+) diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog new file mode 100644 index 0000000..a8b96c9 --- /dev/null +++ b/sci-biology/trinityrnaseq/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/trinityrnaseq +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*trinityrnaseq-20140413 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <[email protected]> + +files/r3590_chmod.patch, +files/sort.patch, +metadata.xml, + +trinityrnaseq-20140413.ebuild: + sci-biology/trinityrnaseq: new package (with last release on sourceforge) diff --git a/sci-biology/trinityrnaseq/files/r3590_chmod.patch b/sci-biology/trinityrnaseq/files/r3590_chmod.patch new file mode 100644 index 0000000..f1bc45e --- /dev/null +++ b/sci-biology/trinityrnaseq/files/r3590_chmod.patch @@ -0,0 +1,24 @@ +--- trinityrnaseq_r20140413p1/trinity-plugins/coreutils/build_parallel_sort.sh 2014-07-03 01:22:30.000000000 +0200 ++++ /home/mmokrejs/tmp/build_parallel_sort.sh 2014-07-03 01:18:35.690493804 +0200 +@@ -29,11 +29,9 @@ + cd ${DIR}/bin + SORTPATH=`which sort` + ln -s ${SORTPATH} +- if [ ! -x ./sort-softlink]; then +- if [ ! -x ${DIR}/bin/sort ]; then ++ if [ ! -x ${DIR}/bin/sort ]; then + chmod +x ${DIR}/bin/sort + fi +- fi + exit 0 + fi + +@@ -56,7 +54,7 @@ + cd ${INSTALLDIR} + ./configure + #make clean +-make -j ++make + cd src + mkdir -p ${DIR}/bin + cp sort ${DIR}/bin diff --git a/sci-biology/trinityrnaseq/files/sort.patch b/sci-biology/trinityrnaseq/files/sort.patch new file mode 100644 index 0000000..c2cccd7 --- /dev/null +++ b/sci-biology/trinityrnaseq/files/sort.patch @@ -0,0 +1,14 @@ +--- trinityrnaseq_r20140413p1/trinity-plugins/coreutils/build_parallel_sort.sh.ori 2014-06-25 10:54:43.000000000 +0200 ++++ trinityrnaseq_r20140413p1/trinity-plugins/coreutils/build_parallel_sort.sh 2014-06-25 10:56:52.000000000 +0200 +@@ -29,7 +29,11 @@ + cd ${DIR}/bin + SORTPATH=`which sort` + ln -s ${SORTPATH} ++ if [ ! -x ./sort-softlink]; then ++ if [ ! -x ${DIR}/bin/sort ]; then + chmod +x ${DIR}/bin/sort ++ fi ++ fi + exit 0 + fi + diff --git a/sci-biology/trinityrnaseq/metadata.xml b/sci-biology/trinityrnaseq/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/trinityrnaseq/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-20140413.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-20140413.ebuild new file mode 100644 index 0000000..a2e497a --- /dev/null +++ b/sci-biology/trinityrnaseq/trinityrnaseq-20140413.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ... +# There is bundled jellyfish-1.1.11 source tree + +DESCRIPTION="Transcriptome assembler for RNA-seq reads" +HOMEPAGE="http://sourceforge.net/projects/trinityrnaseq"; +SRC_URI="http://downloads.sourceforge.net/project/trinityrnaseq/trinityrnaseq_r20140413p1.tar.gz"; + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/trinityrnaseq_r20140413p1 + +src_prepare(){ + epatch "${FILESDIR}"/sort.patch + epatch "${FILESDIR}"/r3590_chmod.patch +} + +src_install(){ + perl_set_version + dobin Trinity util/*.pl util/fasta_tool + dobin Inchworm/bin/* + cd Chrysalis + dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl + cd ${S} || die + insinto ${VENDOR_LIB}/${PN} + dobin util/misc/PerlLib/*.pm PerlLib/*.pm + insinto ${VENDOR_LIB}/${PN}/KmerGraphLib + dobin PerlLib/KmerGraphLib/*.pm + insinto ${VENDOR_LIB}/${PN}/CDNA + dobin PerlLib/CDNA/*.pm + insinto ${VENDOR_LIB}/${PN}/HTC + dobin PerlLib/HTC/*.pm + insinto ${VENDOR_LIB}/${PN}/Simulate + dobin PerlLib/Simulate/*.pm +}
