# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-6.240-r1.ebuild,v 1.2 2008/09/23 15:27:54 mr_bones_ Exp $

EAPI="2"

inherit toolchain-funcs multilib

DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
HOMEPAGE="http://align.bmr.kyushu-u.ac.jp/mafft/software/"
SRC_URI="http://align.bmr.kyushu-u.ac.jp/mafft/software/${P}-with-extensions-src.tgz"

LICENSE="free-noncomm"
SLOT="0"
KEYWORDS="~x86"
IUSE=""

DEPEND=""
RDEPEND=""

S="${WORKDIR}/${P}-with-extensions"

src_unpack() {
	unpack ${A}
	cp ${FILESDIR}/Makefile1 ${S}/extensions/Makefile
	cp ${FILESDIR}/Makefile2 ${S}/extensions/mxscarna_src/Makefile
}

src_compile() {
	emake -C core \
		PREFIX="/usr/$(get_libdir)/${PN}" \
		CC="$(tc-getCC)" \
		CFLAGS="${CFLAGS}" \
		|| die "make core failed"
	emake -C extensions \
		PREFIX="/usr/$(get_libdir)/${PN}" \
		CXX="$(tc-getCXX)" \
		CXXFLAGS="${CXXFLAGS} -I. -IprobconsRNA -Ivienna" \
		|| die "make extensions failed"
}

src_install() {
	emake -C core PREFIX="${D}usr/$(get_libdir)/${PN}" install || die "install failed"
	emake -C extensions PREFIX="${D}usr/$(get_libdir)/${PN}" install || die "install failed"
	insinto "${D}usr/$(get_libdir)/${PN}"
	dobin extensions/mxscarna_src/probconsRNA # install in addition this binary
	dodoc readme
}