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 <[email protected]> + +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 <[email protected]> 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}" +}
