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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
[ "$PV" == "9999" ] && inherit git-r3
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="http://transdecoder.github.io"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
KEYWORDS=""
else
SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz"
KEYWORDS="~amd64"
S="${WORKDIR}"/TransDecoder-"${PV}"
fi
LICENSE="BSD-BroadInstitute"
SLOT="0"
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/cd-hit
sci-biology/parafly
sci-biology/ffindex"
src_prepare(){
rm -rf transdecoder_plugins/cd-hit
for f in PerlLib/*.pm; do
p=`basename $f .pm`;
sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die;
done
epatch "${FILESDIR}"/"${P}"__fix_paths.patch
epatch "${FILESDIR}"/pfam_runner.pl.patch
}
src_compile(){
einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
}
# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
# thread in archives. You can get it from
# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
src_install(){
dobin TransDecoder.Predict TransDecoder.LongOrfs
insinto /usr/share/${PN}/util
doins util/*.pl
chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util || die
# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
rm -rf util/bin
#
# * sci-biology/trinityrnaseq-20140413:0::science
# * /usr/bin/Fasta_reader.pm
# * /usr/bin/GFF3_utils.pm
# * /usr/bin/Gene_obj.pm
# * /usr/bin/Gene_obj_indexer.pm
# * /usr/bin/Longest_orf.pm
# * /usr/bin/Nuc_translator.pm
# * /usr/bin/TiedHash.pm
#
perl_set_version
# this is broken and installs into
# /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/
# instead of
# /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/
insinto ${VENDOR_LIB}/${PN}
doins PerlLib/*.pm
# dodoc Release.Notes
einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
einfo "hmmpress Pfam-A.hmm.bin"
}
pkg_postinst(){
einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
einfo "at least with NCBI blast from either:"
einfo " sci-biology/ncbi-blast+ (released more often) or from"
einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
}
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