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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="Annotation and analysis pipeline for de novo assembled transcriptomes"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}/${PN}-${PN}-v${PV}"
LICENSE="BSD-BroadInstitute"
SLOT="0"
KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/ncbi-tools++
sci-biology/trinityrnaseq
sci-biology/TransDecoder
"
# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
# >=sci-biology/rnammer-2.3.2
#
# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
# >=sci-biology/signalp-4
#
# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'.
# In the 'rnammer' software configuration, edit the rnammer script to point
# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
src_install(){
perl_set_version
dobin Trinotate
insinto /usr/share/"${PN}"
doins -r admin sample_data util TrinotateWeb
perl_domodule -r PerlLib/*
dodoc notes README.md README.txt Changelog.txt
}
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