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

[Andrew Ammerlaan]

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}"
-}