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

1 files changed, 75 insertions, 0 deletions

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 000000000..0d5ba5346
--- /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}"
+}