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92 lines
2.3 KiB
92 lines
2.3 KiB
# Copyright 1999-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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inherit 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="https://www.ebi.ac.uk/~zerbino/velvet/"
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SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
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S="${WORKDIR}"/${MY_P}
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="doc openmp"
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BDEPEND="
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doc? ( virtual/latex-base )
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openmp? (
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|| (
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sys-devel/gcc[openmp]
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sys-devel/clang-runtime[openmp]
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)
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)
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"
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PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" )
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pkg_pretend() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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}
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pkg_setup() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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}
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src_prepare() {
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default
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if ! use doc; then
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sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
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fi
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elog "Upstream recommends using -O3 in CFLAGS"
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echo
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elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters"
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elog "as described in the PDF manual, please set the variables by prepending VELVET_ in"
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elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..."
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elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge"
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elog "the package. For example:"
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elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
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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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use openmp && MAKE_XOPTS+=( OPENMP=1 )
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[[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} )
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[[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} )
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[[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} )
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[[ ! -z "${VELVET_LONGSEQUENCES}" ]] && MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} )
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}
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src_compile() {
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emake "${MAKE_XOPTS[@]}" -j1
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emake "${MAKE_XOPTS[@]}" -j1 color
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}
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src_test() {
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emake "${MAKE_XOPTS[@]}" -j1 test
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}
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src_install() {
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dobin velvet{g,h,g_de,h_de}
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insinto /usr/share/${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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