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author | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-02-01 10:13:31 +0100 |
---|---|---|
committer | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-02-01 10:13:31 +0100 |
commit | 451b8632c92318dc8aec4ec7b625a968c30a28be (patch) | |
tree | 675b0d0d49e3115dd2a34b0aaea2b1ffa0bda62e | |
parent | sci-biology/SOAPdenovo2: version bump 242 (diff) | |
download | sci-451b8632c92318dc8aec4ec7b625a968c30a28be.tar.gz sci-451b8632c92318dc8aec4ec7b625a968c30a28be.tar.bz2 sci-451b8632c92318dc8aec4ec7b625a968c30a28be.zip |
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@riseup.net>
-rw-r--r-- | sci-biology/trinityrnaseq/Manifest | 5 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch | 20 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/files/trinityrnaseq-2.11.0-fix-compilation.patch | 12 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch | 23 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 66 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 75 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild (renamed from sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild) | 37 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 76 |
8 files changed, 31 insertions, 283 deletions
diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest index c8bda9d39..815ffe565 100644 --- a/sci-biology/trinityrnaseq/Manifest +++ b/sci-biology/trinityrnaseq/Manifest @@ -1,4 +1 @@ -DIST trinityrnaseq-2.0.6.tar.gz 158619106 BLAKE2B 9be82099f8c563ac6520462feffcdcb1d0cec7fde4b5d3a430abde987bc419f6011642c1a2548de27734493ac8728e9c24d8a67bd8201108a9b1e26020aca2d6 SHA512 459461db38e42d0b77b9cb84b1ecc4ccb03bbe0fe6e970915d5df58e8c98368a07fab7a157679b0d4247b729b49966b1f3927abee11059e5e3a3406e8e598d45 -DIST trinityrnaseq-2.1.1.tar.gz 137541420 SHA256 012ccb42e1eab8a5b14c4e78becf3e7e69964d76c17fcca8110db6ffe63d3e0b SHA512 36b67211902871c6dbba31a074c4e92d2e925c57fe54bf59418874282e283693d2d9b4e14333385a7adcef3edbf928bc1001df105b56412841662c45a9a74f3f WHIRLPOOL 73869a3f2dbc72011723429d6ac3acb3fde8c7ccfe4122510afbea9fdfc732a457c8f5d16573190448c4e0d2c5dcc437e2f9cfe96f4239368c95b2da79fd52bd -DIST trinityrnaseq-2.2.0.tar.gz 174159736 SHA256 f34603e56ac76a81447dd230b31248d5890ecffee8ef264104d4f1fa7fe46c9e SHA512 87ba299df990d066ae6aa8a870c3a27647da0d78cf0a48c5084967865d4e278ce383b3f6e54541d4626654f0638f12c739aaed04ed770bc99ed84b94c2e6e5c3 WHIRLPOOL 027ccd958288991c4871cfa6b370d14bc2bf586bc1ffc3247795aaf305368caac373343682f11cde6d72a65422c95718b89fee65ac77c04a21c7c3aaa4c8112d -DIST trinityrnaseq-2.6.6.tar.gz 21796945 BLAKE2B 0d5ff2d7e2ba11d231695c19e0125d507a5f510a944fc3ab68c3e5073b6bb4ef0973bc02b207b79ea6adbc58a469eeb894610bd765c11ccf3963deaeebe3ff00 SHA512 2e4438010cc987706b8f7dd343cdd84024318f2e7370bce40be6d54b07b17bfd6a4a28c27400250384e4ffd560386fde3b9c51987f86b376e11c4daa10d6b7cb +DIST trinityrnaseq-2.11.0.tar.gz 320752461 BLAKE2B 53327a49d31f7350e8fe820ac106f1cbe0577097852a63ea2154004d1945079f737f646c09d9907cfd45fb011845ea5e21eedf8fcda09e1db17d563fbdd0fd66 SHA512 9e9af2a16423ff8c063522c7acb6c8fc9386a95a7b58e01c94cd97971f71c3080cd5b2d34133bb501505d35cae05b77ff8423ad948324f49f9d4ddbb16629d20 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 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}" -} |