commit: cd5ffe2b8f606c841206f700c8718f5c3b7fda9e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 10:52:33 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 10:52:33 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cd5ffe2b
sci-biology/trinityrnaseq: version bump; dropped patches because target file is
gone; ideally should depend on <sci-biology/samtools-1.1 but lets see what are
the real requirements
Package-Manager: portage-2.2.18
sci-biology/trinityrnaseq/ChangeLog | 9 ++++
sci-biology/trinityrnaseq/files/r3590_chmod.patch | 24 ---------
sci-biology/trinityrnaseq/files/sort.patch | 14 -----
.../trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 63 ++++++++++++++++++++++
.../trinityrnaseq/trinityrnaseq-20140413.ebuild | 49 -----------------
5 files changed, 72 insertions(+), 87 deletions(-)
diff --git a/sci-biology/trinityrnaseq/ChangeLog
b/sci-biology/trinityrnaseq/ChangeLog
index a8b96c9..a630ba3 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -2,6 +2,15 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*trinityrnaseq-2.0.6 (30 Apr 2015)
+
+ 30 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz>
+ +trinityrnaseq-2.0.6.ebuild, -files/r3590_chmod.patch, -files/sort.patch,
+ -trinityrnaseq-20140413.ebuild:
+ sci-biology/trinityrnaseq: version bump; dropped patches because target file
+ is gone; ideally should depend on <sci-biology/samtools-1.1 but lets see what
+ are the real requirements
+
*trinityrnaseq-20140413 (30 Apr 2015)
30 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz>
diff --git a/sci-biology/trinityrnaseq/files/r3590_chmod.patch
b/sci-biology/trinityrnaseq/files/r3590_chmod.patch
deleted file mode 100644
index f1bc45e..0000000
--- a/sci-biology/trinityrnaseq/files/r3590_chmod.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- 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
deleted file mode 100644
index c2cccd7..0000000
--- a/sci-biology/trinityrnaseq/files/sort.patch
+++ /dev/null
@@ -1,14 +0,0 @@
----
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/trinityrnaseq-2.0.6.ebuild
b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
new file mode 100644
index 0000000..335d075
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -0,0 +1,63 @@
+# 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://trinityrnaseq.github.io/";
+SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/parafly
+ =sci-biology/jellyfish-2.1.4
+ sci-biology/samtools
+ dev-perl/IO-All"
+# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
+# version of bundled jellyfish is 2.1.4
+
+#src_compile(){
+# emake all
+# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool,
parafly
+#}
+
+src_install(){
+ perl_set_version
+ dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool
+ # should become a new package depending on dev-perl/IO-All
+ dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
+ dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
+ #
+ insinto /usr/share/${PN}/util
+ doins -r util/*
+ #
+ 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}
+ doins util/misc/PerlLib/*.pm PerlLib/*.pm
+ insinto ${VENDOR_LIB}/${PN}/KmerGraphLib
+ doins PerlLib/KmerGraphLib/*.pm
+ insinto ${VENDOR_LIB}/${PN}/CDNA
+ doins PerlLib/CDNA/*.pm
+ insinto ${VENDOR_LIB}/${PN}/HPC
+ doins PerlLib/HPC/*.pm
+ insinto ${VENDOR_LIB}/${PN}/Simulate
+ doins PerlLib/Simulate/*.pm
+ insinto ${VENDOR_LIB}/${PN}/CanvasXpress
+ doins PerlLib/CanvasXpress/*.pm
+ chmod a+rx -R ${ED}/${VENDOR_LIB}/${PN}
+}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-20140413.ebuild
b/sci-biology/trinityrnaseq/trinityrnaseq-20140413.ebuild
deleted file mode 100644
index a2e497a..0000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-20140413.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# 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
-}
