[gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/files/, sci-biology/trinityrnaseq/

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.cz>
+  +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>mmokrejs@×××××××××××××××.cz</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
+}