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

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.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 <mmokrejs@×××××××××××××××.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
-}