sci-biology/bowtie/bowtie-0.12.7.ebuild


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# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.12.7.ebuild,v 1.1 2011/03/06 17:18:05 jlec Exp $

EAPI="4"

inherit toolchain-funcs

DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"

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

DEPEND="app-arch/unzip"
RDEPEND=""

# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS

#src_prepare() {
#	sed -i 's/$(CXX) $(RELEASE_FLAGS)/$(CXX) $(CXXFLAGS) $(RELEASE_FLAGS)/' "${S}/Makefile" || die
#}

src_compile() {
	unset CFLAGS
	emake \
		CC="$(tc-getCC)" \
		CPP="$(tc-getCXX)" \
		CXX="$(tc-getCXX)" \
		EXTRA_FLAGS="${LDFLAGS}" \
		RELEASE_FLAGS=""
}

src_install() {
	dobin bowtie bowtie-* || die
	exeinto /usr/share/${PN}/scripts
	doexe scripts/* || die
	newman MANUAL bowtie.1
	dodoc AUTHORS NEWS TUTORIAL
}