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# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
inherit eutils
MY_P="MUMmer${PV}"
DESCRIPTION="A rapid whole genome aligner"
HOMEPAGE="http://mummer.sourceforge.net/"
SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
IUSE="doc"
KEYWORDS="amd64 x86"
DEPEND=""
RDEPEND="app-shells/tcsh"
S="${WORKDIR}/${MY_P}"
src_unpack() {
unpack ${A}
cd "${S}"
epatch "${FILESDIR}"/${P}-gcc43.patch
# Warning: package uses CPPFLAGS on c in addition to cpp, despite the name
sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
-e 's/LDFLAGS =$//' "${S}/Makefile"
}
src_compile() {
emake || die "emake failed"
sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
-e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
-e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
-e 's|\(set bindir = \).*|\1/usr/bin|' \
-e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
-e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
}
src_install() {
dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
exact-tandems promer repeat-match show-aligns gaps mummer \
show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die
newbin annotate mummer-annotate || die
insinto /usr/share/${PN}/scripts
doins scripts/{*.awk,*.csh,*.pl}
insinto /usr/share/${PN}/lib
doins scripts/Foundation.pm || die
dodoc ACKNOWLEDGEMENTS ChangeLog README
insinto /usr/share/doc/${PF}
use doc && doins -r docs
}
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