| # 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 |
| } |