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# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
inherit eutils flag-o-matic toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip"
LICENSE="GPL-3"
SLOT="2"
IUSE="sse2 examples"
KEYWORDS="~amd64 ~x86"
CDEPEND="dev-lang/perl"
DEPEND="${CDEPEND} \
app-arch/unzip"
RDEPEND="${CDEPEND}"
S="${WORKDIR}/${PN}2-${PV}"
pkg_pretend() {
if ! use sse2 ; then
ebegin
eerror "bowtie2 requires sse2 support. Please make sure your system supports"
eerror "sse2 and enable the sse2 use flag."
eend
die
fi
}
src_prepare() {
epatch "${FILESDIR}/${P}-buildsystem.patch"
}
src_compile() {
use sse2 && append-cxxflags -msse2
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS}"
}
src_install() {
dobin bowtie2 bowtie2-*
exeinto /usr/share/${PN}2/scripts
doexe scripts/*
newman MANUAL bowtie2.1
dodoc AUTHORS NEWS TUTORIAL
dohtml doc/manual.html doc/style.css
if use examples; then
insinto /usr/share/${PN}2
doins -r example
fi
}
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