# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/mummer-3.22-r1.ebuild,v 1.1 2011/01/13 09:14:52 jlec Exp $

EAPI="3"

inherit eutils flag-o-matic

DESCRIPTION="A rapid whole genome aligner"
HOMEPAGE="http://mummer.sourceforge.net/"
SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz"

LICENSE="Artistic"
SLOT="0"
IUSE="doc"
KEYWORDS="~amd64 ~x86"

DEPEND=""
RDEPEND="app-shells/tcsh"

S="${WORKDIR}/MUMmer${PV}"

src_prepare() {
	use amd64 && append-flags -DSIXTYFOURBITS

	epatch \
		"${FILESDIR}"/${PV}-prll.patch \
		"${FILESDIR}"/${PV}-ldflags.patch

	sed \
		-e '/^CFLAGS/d' \
		-e '/^CXXFLAGS/d' \
		-e '/^LDFLAGS/d' \
		-i Makefile || die
}

src_compile() {
	emake || die

	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/'${PN}'/lib"|' \
		scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die
	mv annotate mummer-annotate || die
	sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die
}

src_install() {
	dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die

	insinto /usr/share/${PN}/scripts
	doins scripts/{*.awk,*.csh,*.pl} || die
	insinto /usr/share/${PN}/lib
	doins scripts/Foundation.pm || die

	dodoc ACKNOWLEDGEMENTS ChangeLog README || die
	insinto /usr/share/doc/${PF}
	if use doc; then
		doins -r docs || die
	fi
}