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# Copyright 1999-2015 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
DESCRIPTION="HMM-based cDNA to genome aligner"
HOMEPAGE="http://mblab.wustl.edu/software.html"
SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar"
LICENSE="BSD-2"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
DEPEND="dev-lang/perl"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/pairagon
src_prepare(){
sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' -i Makefile
sed -e 's/^use Alignment/use pairagon::Alignment/' -i bin/alignmentConvert.pl || die
}
src_compile(){
emake pairagon-linux
}
src_install(){
dobin bin/pairagon bin/pairameter_estimate bin/Pairagon.pl bin/alignmentConvert.pl
dodoc README
perl_set_version
insinto /usr/share/pairagon
doins parameters/*
insinto ${VENDOR_LIB}/${PN}
doins lib/perl5/Alignment.pm
}
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