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