# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$

EAPI="2"

DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
HOMEPAGE="https://code.google.com/p/mosaik-aligner/"
SRC_URI="https://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2"

LICENSE="GPL-2"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"

DEPEND=""
RDEPEND=""

S="${WORKDIR}/mosaik-aligner"

src_prepare() {
	sed -i 's/-static//' src/includes/linux.inc || die
}

src_compile() {
	emake -C src || die
#	emake -C MosaikTools/c++ || die
#	emake -C MosaikTools/perl || die
}

src_install() {
	dobin bin/* || die

	insinto /usr/share/${PN}
	doins -r MosaikTools || die

	dodoc README Mosaik-1.0-Documentation.pdf
}