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# 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/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
>=sci-biology/jellyfish-2.2.6:2
>=sci-libs/htslib-1.2.1
>=sci-biology/samtools-1.3:0
>=sci-biology/trimmomatic-0.36
>=sci-biology/GAL-0.2.1
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 "${FILESDIR}"/"${P}"-disable_some_plugins.patch
}
#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 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
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}/${PN}"
doins util/misc/PerlLib/*.pm PerlLib/*.pm
insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib
doins PerlLib/KmerGraphLib/*.pm
insinto "${VENDOR_LIB}/${PN}"/CDNA
doins PerlLib/CDNA/*.pm
insinto "${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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