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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit eutils toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
KEYWORDS="amd64 x86 ~x64-macos"
IUSE="examples +tbb"
DEPEND="app-arch/unzip
tbb? ( dev-cpp/tbb )"
RDEPEND=""
DOCS=( AUTHORS NEWS TUTORIAL doc/README )
HTML_DOCS=( doc/{manual.html,style.css} )
src_prepare() {
# always include tinythread.cpp
epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
}
src_compile() {
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
CFLAGS="" \
CXXFLAGS="" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS}" \
WITH_TBB="$(usex tbb 1 0)"
}
src_install() {
dobin ${PN} ${PN}-*
exeinto /usr/libexec/${PN}
doexe scripts/*
newman MANUAL ${PN}.1
einstalldocs
if use examples; then
insinto /usr/share/${PN}
doins -r genomes indexes
fi
}
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