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# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI="2"
inherit eutils
MY_P="lagan20"
DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
DEPEND=""
RDEPEND=""
S="${WORKDIR}/${MY_P}"
src_prepare() {
sed -i "/use Getopt::Long;/ i use lib \"/usr/share/${PN}/lib\";" "${S}/supermap.pl" || die
# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
epatch "${FILESDIR}"/${P}-*.patch
}
src_install() {
dobin lagan.pl slagan.pl mlagan
rm lagan.pl slagan.pl utils/Utils.pm
dodir /usr/share/${PN}/lib
insinto /usr/share/${PN}/lib
doins Utils.pm
exeinto /usr/share/${PN}/utils
doexe utils/*
exeinto /usr/share/${PN}
doexe *.pl anchors chaos glocal order prolagan
insinto /usr/share/${PN}
doins *.txt
dosym /usr/share/${PN}/supermap.pl /usr/bin/supermap
dosym /usr/bin/lagan.pl /usr/bin/lagan
dosym /usr/bin/slagan.pl /usr/bin/slagan
echo "LAGAN_DIR=\"/usr/share/${PN}\"" > ${S}/99${PN}
doenvd "${S}/99${PN}"
dodoc Readmes/README.*
}
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