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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit perl-functions 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}/${PN}
src_prepare() {
default
sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' \
-i Makefile || die
sed -e 's/^use Alignment/use pairagon::Alignment/' \
-i bin/alignmentConvert.pl || die
}
src_compile() {
emake pairagon-linux
}
src_install() {
dobin bin/{pairagon,pairameter_estimate,Pairagon.pl,alignmentConvert.pl}
einstalldocs
insinto /usr/share/pairagon
doins -r parameters/.
perl_domodule -C ${PN} lib/perl5/Alignment.pm
}
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