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76 lines
1.6 KiB
76 lines
1.6 KiB
9 years ago
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# Copyright 1999-2016 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=6
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inherit flag-o-matic 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/${P}-src.zip"
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LICENSE="Artistic"
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SLOT="1"
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KEYWORDS="~amd64 ~x86 ~x64-macos"
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IUSE="examples +tbb"
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RDEPEND="tbb? ( dev-cpp/tbb )"
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DEPEND="${RDEPEND}
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sci-biology/seqan:1.4
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app-arch/unzip"
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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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PATCHES=(
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"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
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"${FILESDIR}/${P}-fix-setBegin-call.patch"
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"${FILESDIR}/${P}-seqan-popcount.patch"
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"${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
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"${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
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"${FILESDIR}/${P}-spelling.patch"
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"${FILESDIR}/${P}-tbb-tinythread-missing.patch"
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"${FILESDIR}/${P}-unbundle-seqan.patch"
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)
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src_prepare() {
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default
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# remove bundled libraries, use system seqan 1.4
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rm -rf SeqAn-1.1/ third_party/ || die
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# innocuous non-security flags, prevent log pollution
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append-cxxflags \
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-Wno-unused-local-typedefs \
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-Wno-unused-but-set-variable \
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-Wno-unused-variable
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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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