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