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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit perl-module
DESCRIPTION="Transcriptome assembler for RNA-seq reads"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}/${PN}-v${PV}"
LICENSE="BSD-BroadInstitute"
SLOT="0"
KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/parafly
>=sci-biology/jellyfish-2.2.6:2
>=sci-libs/htslib-1.2.1
>=sci-biology/samtools-1.3:0
>=sci-biology/trimmomatic-0.36
>=sci-biology/GAL-0.2.1
dev-perl/IO-All
sci-biology/seqtools
"
PATCHES=(
"${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
)
src_compile(){
# missing submodule for bamsifter
emake no_bamsifter
emake plugins
}
src_install(){
# fix the install path
sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \
-i util/support_scripts/trinity_installer.py || die
dodir /usr/bin
default
}
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