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}"
-}
