* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/files/, sci-biology/trinityrnaseq/
@ 2015-04-30 9:26 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-04-30 9:26 UTC (permalink / raw
To: gentoo-commits
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@fold.natur.cuni.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@fold.natur.cuni.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
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/files/, sci-biology/trinityrnaseq/
@ 2015-11-20 23:56 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-11-20 23:56 UTC (permalink / raw
To: gentoo-commits
commit: e1a9394386238099ece40fe0e8d7f805c23b679d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 20 23:54:55 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 20 23:54:55 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1a93943
sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we relocate *.pm file into vendor_perl and all 'use blah' calls to trinity-provided perl modules need to be changed to 'use trinityrnaseq::blah', or PERL5INC modified?
Package-Manager: portage-2.2.18
sci-biology/trinityrnaseq/ChangeLog | 9 +++
.../trinityrnaseq/files/disable_some_plugins.patch | 20 ++++++
.../trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 75 ++++++++++++++++++++++
3 files changed, 104 insertions(+)
diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index 0376bce..405ac83 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
# $Id$
+*trinityrnaseq-2.1.1 (20 Nov 2015)
+
+ 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/disable_some_plugins.patch, +trinityrnaseq-2.1.1.ebuild:
+ sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we
+ relocate *.pm file into vendor_perl and all 'use blah' calls to trinity-
+ provided perl modules need to be changed to 'use trinityrnaseq::blah', or
+ PERL5INC modified?
+
06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml
diff --git a/sci-biology/trinityrnaseq/files/disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/disable_some_plugins.patch
new file mode 100644
index 0000000..43a06ae
--- /dev/null
+++ b/sci-biology/trinityrnaseq/files/disable_some_plugins.patch
@@ -0,0 +1,20 @@
+--- trinityrnaseq-2.1.1/trinity-plugins/Makefile.ori 2015-11-21 00:34:52.310075544 +0100
++++ trinityrnaseq-2.1.1/trinity-plugins/Makefile 2015-11-21 00:37:16.260075920 +0100
+@@ -10,7 +10,7 @@
+ PARAFLY_CODE=parafly-code
+ TRIMMOMATIC_CODE=Trimmomatic-0.32
+
+-trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
++trinity_essentials: scaffold_iworm_contigs_target fastool_target parafly_target
+
+ trimmomatic_target:
+ ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+@@ -31,7 +31,7 @@
+ # cd htslib-1.2.1 && ./configure && $(MAKE)
+ tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
+
+-scaffold_iworm_contigs_target: htslib_target
++scaffold_iworm_contigs_target:
+ cd scaffold_iworm_contigs && $(MAKE)
+
+ fastool_target:
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
new file mode 100644
index 0000000..0d5ba53
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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 ...
+
+DESCRIPTION="Transcriptome assembler for RNA-seq reads"
+HOMEPAGE="http://trinityrnaseq.github.io/"
+SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/parafly
+ =sci-biology/jellyfish-2.1.4
+ >=sci-libs/htslib-1.2.1
+ <=sci-biology/samtools-1.1
+ >=sci-biology/trimmomatic-0.32
+ dev-perl/IO-All"
+# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
+# version of bundled jellyfish is 2.1.4
+# version of bundled samtools is 0.1.19
+# version of bundled htslib is 1.2.1
+# version of bundled GAL is 0.2.1
+# version of bundled trimmomatic is 0.32
+
+# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
+
+src_prepare(){
+ epatch "${FILESDIR}"/disable_some_plugins.patch
+}
+
+#src_compile(){
+# emake all
+# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
+#}
+
+src_install(){
+ perl_set_version
+ dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool
+ # should become a new package depending on dev-perl/IO-All
+ dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
+ dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
+ #
+ insinto /usr/share/"${PN}"/util
+ rm -f util/fasta_tool
+ 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}"
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/files/, sci-biology/trinityrnaseq/
@ 2018-04-21 18:53 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-04-21 18:53 UTC (permalink / raw
To: gentoo-commits
commit: 2dffd7378f16086d11d32432d30d0325d40d3238
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 18:53:23 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 18:53:23 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2dffd737
sci-biology/trinityrnaseq: version bump (no KEYWORDS set)
The perl include paths are not matching the paths in *.pm files
all *.pm need to be patched so that they could be placed into
site_perl subdirectory.
In brief, the package still does not support installation into
a site-wide directory. users are supposed to executed off the
unpacked tarball directly.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
...trinityrnaseq-2.1.1-disable_some_plugins.patch} | 0
.../trinityrnaseq-2.6.6-disable_some_plugins.patch | 23 ++++++++++
.../trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 4 +-
.../trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 4 +-
.../trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 4 +-
...seq-2.1.1.ebuild => trinityrnaseq-2.6.6.ebuild} | 53 +++++++++++-----------
6 files changed, 56 insertions(+), 32 deletions(-)
diff --git a/sci-biology/trinityrnaseq/files/disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
similarity index 100%
rename from sci-biology/trinityrnaseq/files/disable_some_plugins.patch
rename to sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
new file mode 100644
index 000000000..02f4d5d8a
--- /dev/null
+++ b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
@@ -0,0 +1,23 @@
+--- trinity-plugins/Makefile 2018-04-21 20:01:58.389880915 +0200
++++ trinity-plugins/Makefile 2018-04-21 20:03:31.752684954 +0200
+@@ -7,7 +7,7 @@
+
+
+
+-trinity_essentials: seqtk_target parafly_target trimmomatic_target
++trinity_essentials: parafly_target
+
+ trimmomatic_target:
+ ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+@@ -39,11 +39,9 @@
+ cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf ${COLLECTL_CODE} collectl
+
+ clean:
+- rm -rf ./seqtk-trinity-0.0.2
+ cd scaffold_iworm_contigs && $(MAKE) clean
+ cd parafly-code && $(MAKE) clean
+ rm -f ./parafly # rm symlink
+- rm -f ./Trimmomatic # rm symlink
+ cd slclust && $(MAKE) clean
+ cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
+ @echo "\n\n** Done cleaning plugins area **"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
index 95a9ae58d..1941db22a 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -21,7 +21,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4:2
sci-biology/samtools:0.1-legacy
>=sci-biology/GAL-0.2.1
dev-perl/IO-All"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
index 952d3a41a..8f131cb17 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -20,7 +20,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4:2
>=sci-libs/htslib-1.2.1
sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
index a6692a0ec..19085d752 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -20,7 +20,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.1.4:2
>=sci-libs/htslib-1.2.1
sci-biology/samtools:0.1-legacy
>=sci-biology/trimmomatic-0.32
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
similarity index 52%
copy from sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
copy to sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
index 952d3a41a..238766eed 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -10,33 +10,34 @@ inherit perl-module eutils toolchain-funcs
DESCRIPTION="Transcriptome assembler for RNA-seq reads"
HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4
+ >=sci-biology/jellyfish-2.2.6:2
>=sci-libs/htslib-1.2.1
- sci-biology/samtools:0.1-legacy
- >=sci-biology/trimmomatic-0.32
+ >=sci-biology/samtools-1.3:0
+ >=sci-biology/trimmomatic-0.36
>=sci-biology/GAL-0.2.1
- dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-# version of bundled samtools is 0.1.19
-# version of bundled htslib is 1.2.1
-# version of bundled GAL is 0.2.1
-# version of bundled trimmomatic is 0.32
-
+ dev-perl/IO-All
+ sci-biology/seqtools"
# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
+# has the following "plugins" (aka bundled 3rd-party code)
+# slclust
+# DEXseq_util
+# COLLECTL
+# ParaFly-0.1.0
+
+S="${WORKDIR}"/trinityrnaseq-Trinity-v"${PV}"
src_prepare(){
- epatch "${FILESDIR}"/disable_some_plugins.patch
+ epatch "${FILESDIR}"/"${P}"-disable_some_plugins.patch
}
#src_compile(){
@@ -45,19 +46,21 @@ src_prepare(){
#}
src_install(){
+ dodoc Chrysalis/chrysalis.notes
+ dodoc Changelog.txt
perl_set_version
dobin Trinity util/*.pl
- # should become a new package depending on dev-perl/IO-All
- dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
- dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
- #
- insinto /usr/share/"${PN}"/util
- rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
- doins -r util/*
- #
dobin Inchworm/bin/*
cd Chrysalis || die
- dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
+ dobin MakeDepend checkLock BreakTransByPairs BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta GraphFromFasta_MPI IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts ReadsToTranscripts_MPI ReadsToTranscripts_MPI_chang RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
+ cd ../util/R || die
+ insinto /usr/share/"${PN}"/R
+ doins *.R
+ cd ../PBS || die
+ insinto /usr/share/"${PN}"/PBS
+ doins *
+ cd .. || die
+ cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
cd "${S}" || die
insinto "${VENDOR_LIB}/${PN}"
doins util/misc/PerlLib/*.pm PerlLib/*.pm
@@ -65,8 +68,6 @@ src_install(){
doins PerlLib/KmerGraphLib/*.pm
insinto "${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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/files/, sci-biology/trinityrnaseq/
@ 2021-02-01 9:14 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 9:14 UTC (permalink / raw
To: gentoo-commits
commit: 451b8632c92318dc8aec4ec7b625a968c30a28be
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 09:13:31 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 09:13:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=451b8632
sci-biology/trinityrnaseq: version bump 2.11.0
no keywords, because dep GAL is missing them
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../trinityrnaseq-2.1.1-disable_some_plugins.patch | 20 ------
.../trinityrnaseq-2.11.0-fix-compilation.patch | 12 ++++
.../trinityrnaseq-2.6.6-disable_some_plugins.patch | 23 -------
.../trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 66 -------------------
.../trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 75 ---------------------
...eq-2.6.6.ebuild => trinityrnaseq-2.11.0.ebuild} | 37 +++++------
.../trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 76 ----------------------
7 files changed, 30 insertions(+), 279 deletions(-)
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
deleted file mode 100644
index 43a06ae53..000000000
--- a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- trinityrnaseq-2.1.1/trinity-plugins/Makefile.ori 2015-11-21 00:34:52.310075544 +0100
-+++ trinityrnaseq-2.1.1/trinity-plugins/Makefile 2015-11-21 00:37:16.260075920 +0100
-@@ -10,7 +10,7 @@
- PARAFLY_CODE=parafly-code
- TRIMMOMATIC_CODE=Trimmomatic-0.32
-
--trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
-+trinity_essentials: scaffold_iworm_contigs_target fastool_target parafly_target
-
- trimmomatic_target:
- ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
-@@ -31,7 +31,7 @@
- # cd htslib-1.2.1 && ./configure && $(MAKE)
- tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
-
--scaffold_iworm_contigs_target: htslib_target
-+scaffold_iworm_contigs_target:
- cd scaffold_iworm_contigs && $(MAKE)
-
- fastool_target:
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch
new file mode 100644
index 000000000..8647aad3a
--- /dev/null
+++ b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch
@@ -0,0 +1,12 @@
+diff --git a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
+index e8ecbcf..ccdbd27 100644
+--- a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
++++ b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
+@@ -10,6 +10,7 @@
+ #include <set>
+ #include <utility>
+ #include <vector>
++#include <string>
+
+ #include "htslib/sam.h"
+ #include "htslib/bgzf.h"
diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
deleted file mode 100644
index 02f4d5d8a..000000000
--- a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch
+++ /dev/null
@@ -1,23 +0,0 @@
---- trinity-plugins/Makefile 2018-04-21 20:01:58.389880915 +0200
-+++ trinity-plugins/Makefile 2018-04-21 20:03:31.752684954 +0200
-@@ -7,7 +7,7 @@
-
-
-
--trinity_essentials: seqtk_target parafly_target trimmomatic_target
-+trinity_essentials: parafly_target
-
- trimmomatic_target:
- ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
-@@ -39,11 +39,9 @@
- cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf ${COLLECTL_CODE} collectl
-
- clean:
-- rm -rf ./seqtk-trinity-0.0.2
- cd scaffold_iworm_contigs && $(MAKE) clean
- cd parafly-code && $(MAKE) clean
- rm -f ./parafly # rm symlink
-- rm -f ./Trimmomatic # rm symlink
- cd slclust && $(MAKE) clean
- cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
- @echo "\n\n** Done cleaning plugins area **"
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
deleted file mode 100644
index 1941db22a..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-# There is bundled jellyfish-1.1.11 source tree
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4:2
- sci-biology/samtools:0.1-legacy
- >=sci-biology/GAL-0.2.1
- dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-
-#src_compile(){
-# emake all
-# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
- perl_set_version
- dobin Trinity util/*.pl
- # 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/"${PN}"/util
- rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
- doins -r util/*
- #
- dobin Inchworm/bin/*
- cd Chrysalis || die
- dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
- cd "${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}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
deleted file mode 100644
index 05759d02d..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4:2
- >=sci-libs/htslib-1.2.1
- sci-biology/samtools:0.1-legacy
- >=sci-biology/trimmomatic-0.32
- >=sci-biology/GAL-0.2.1
- dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-# version of bundled samtools is 0.1.19
-# version of bundled htslib is 1.2.1
-# version of bundled GAL is 0.2.1
-# version of bundled trimmomatic is 0.32
-
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-
-src_prepare(){
- epatch "${FILESDIR}"/trinityrnaseq-2.1.1-disable_some_plugins.patch
-}
-
-#src_compile(){
-# emake all
-# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
- perl_set_version
- dobin Trinity util/*.pl
- # should become a new package depending on dev-perl/IO-All
- dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
- dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
- #
- insinto /usr/share/"${PN}"/util
- rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
- doins -r util/*
- #
- dobin Inchworm/bin/*
- cd Chrysalis || die
- 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-2.6.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
similarity index 63%
rename from sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
rename to sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
index 238766eed..4fd8dac9a 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
@@ -1,21 +1,19 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module toolchain-funcs
# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.tar.gz -> ${P}.tar.gz"
+HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
+SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
-IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
@@ -34,26 +32,27 @@ RDEPEND="${DEPEND}
# COLLECTL
# ParaFly-0.1.0
-S="${WORKDIR}"/trinityrnaseq-Trinity-v"${PV}"
+S="${WORKDIR}/${PN}-v${PV}"
-src_prepare(){
- epatch "${FILESDIR}"/"${P}"-disable_some_plugins.patch
-}
+PATCHES=(
+ "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
+)
-#src_compile(){
-# emake all
-# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
+src_compile(){
+ emake all
+ emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
+}
src_install(){
dodoc Chrysalis/chrysalis.notes
dodoc Changelog.txt
perl_set_version
- dobin Trinity util/*.pl
+ dobin Trinity
+ perl_domodule util/*.pl
dobin Inchworm/bin/*
- cd Chrysalis || die
- dobin MakeDepend checkLock BreakTransByPairs BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta GraphFromFasta_MPI IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts ReadsToTranscripts_MPI ReadsToTranscripts_MPI_chang RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
- cd ../util/R || die
+ cd Chrysalis/bin || die
+ dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts
+ cd ../../util/R || die
insinto /usr/share/"${PN}"/R
doins *.R
cd ../PBS || die
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
deleted file mode 100644
index 6d8da6ab9..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="http://trinityrnaseq.github.io/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/parafly
- >=sci-biology/jellyfish-2.1.4:2
- >=sci-libs/htslib-1.2.1
- sci-biology/samtools:0.1-legacy
- >=sci-biology/trimmomatic-0.32
- >=sci-biology/GAL-0.2.1
- dev-perl/IO-All"
-# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
-# version of bundled jellyfish is 2.1.4
-# version of bundled samtools is 0.1.19
-# version of bundled htslib is 1.2.1
-# version of bundled GAL is 0.2.1
-# version of bundled trimmomatic is 0.32
-
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-
-src_prepare(){
- epatch "${FILESDIR}"/trinityrnaseq-2.1.1-disable_some_plugins.patch
-}
-
-#src_compile(){
-# emake all
-# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-#}
-
-src_install(){
- perl_set_version
- dobin Trinity util/*.pl
- # should become a new package depending on dev-perl/IO-All
- dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
- dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
- #
- # https://github.com/trinityrnaseq/trinityrnaseq/issues/126
- insinto /usr/share/"${PN}"/util
- rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool
- doins -r util/*
- #
- dobin Inchworm/bin/*
- cd Chrysalis || die
- 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}"
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2021-02-01 9:14 UTC | newest]
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2018-04-21 18:53 [gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/files/, sci-biology/trinityrnaseq/ Martin Mokrejs
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2021-02-01 9:14 Andrew Ammerlaan
2015-11-20 23:56 Martin Mokrejs
2015-04-30 9:26 Martin Mokrejs
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