# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/bwa-0.7.12.ebuild,v 1.3 2015/04/19 09:59:46 ago Exp $

EAPI=5

inherit eutils toolchain-funcs

DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
HOMEPAGE="http://bio-bwa.sourceforge.net/"
SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"

LICENSE="GPL-3"
SLOT="0"
IUSE=""
KEYWORDS="amd64 x86 ~x64-macos"

PATCHES=( "${FILESDIR}"/${P}-Makefile.patch )

src_prepare() {
	epatch ${PATCHES[@]}
	tc-export CC AR
}

src_install() {
	dobin bwa

	doman bwa.1

	exeinto /usr/libexec/${PN}
	doexe qualfa2fq.pl xa2multi.pl

	dodoc NEWS.md README-alt.md README.md
}