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# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI="2"
inherit eutils multilib toolchain-funcs
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/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
S="${WORKDIR}/${MY_P}"
src_prepare() {
sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${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}"/${P}-*.patch
}
src_compile() {
emake \
CC=$(tc-getCC) \
CXX=$(tc-getCXX) \
CXXFLAGS="${CXXFLAGS}" \
CFLAGS="${CFLAGS}"
}
src_install() {
newbin lagan.pl lagan || die
newbin slagan.pl slagan || die
dobin mlagan || die
rm lagan.pl slagan.pl utils/Utils.pm
insinto /usr/$(get_libdir)/${PN}/lib
doins Utils.pm || die
exeinto /usr/$(get_libdir)/${PN}/utils
doexe utils/* || die
exeinto /usr/$(get_libdir)/${PN}
doexe *.pl anchors chaos glocal order prolagan || die
insinto /usr/$(get_libdir)/${PN}
doins *.txt || die
dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > ${S}/99${PN}
doenvd "${S}/99${PN}" || die
dodoc Readmes/README.* || die
}
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