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# Copyright 1999-2017 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
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}"
}
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