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# Copyright 1999-2013 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=5
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inherit eutils flag-o-matic toolchain-funcs
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MY_P=${PN}_${PV}
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DESCRIPTION="A sequence assembler for very short reads"
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HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
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SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="doc openmp"
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RDEPEND=""
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DEPEND="${RDEPEND}
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doc? ( virtual/latex-base )"
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S="${WORKDIR}"/${MY_P}
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src_prepare() {
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if ! use doc; then
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sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
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fi
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elog "Upstream recommendes using -O3 in CFLAGS"
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echo
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elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
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elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
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elog "environment or /etc/make.conf, then re-emerge the package. For example:"
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elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
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MAKEOPTS+=" -j1"
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if [[ $(tc-getCC) =~ gcc ]]; then
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local eopenmp=-fopenmp
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elif [[ $(tc-getCC) =~ icc ]]; then
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local eopenmp=-openmp
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else
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elog "Cannot detect compiler type so not setting openmp support"
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fi
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append-flags -fPIC ${eopenmp}
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append-ldflags ${eopenmp}
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tc-export CC
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MAKE_XOPTS=(
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CC=$(tc-getCC)
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CFLAGS="${CFLAGS}"
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OPT="${CFLAGS}"
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)
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if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
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if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
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}
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src_compile() {
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emake "${MAKE_XOPTS[@]}"
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emake "${MAKE_XOPTS[@]}" color
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}
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src_test() {
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emake "${MAKE_XOPTS[@]}" test
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}
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src_install() {
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dobin velvet{g,h,g_de,h_de}
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insinto /usr/share/${PN}
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doins -r contrib
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dodoc Manual.pdf CREDITS.txt ChangeLog
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}
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