# 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 ~amd64"
IUSE=""

DEPEND=""
RDEPEND=""

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

src_unpack() {
	unpack ${A}
}

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

src_install() {
	dobin core/mafft core/mafft-homologs.rb || die "dobin failed"

	echo "Creating symlinks to mafft executable"
	pushd "${D}"usr/bin
	for f in linsi ginsi fftns fftnsi nwns nwnsi einsi mafft-linsi mafft-ginsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-einsi mafft-xinsi mafft-qinsi; do ln -s mafft $f; done
	ln -s ../lib/mafft/mafft-profile .
	ln -s ../lib/mafft/mafft-distance .
	popd

	cd core
	insinto usr/lib/mafft
	doins dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen score getlag dndpre dndpre2 setcore || die "Cannot install executables into /usr/lib/mafft"
	doman mafft.1 mafft-homologs.1 || die "Cannot install man pages"

	cd ../extensions
	doins mxscarnamod || die "Cannot install modifiedmxscarna binary"

	echo "Fixing the permissions on executables"
	chmod a+rx "${D}"usr/lib/mafft/*

	cd ..
	dodoc readme || die "Installing readme file failed"
}