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# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit flag-o-matic toolchain-funcs
MY_P="${PN}_${PV}"
DESCRIPTION="A sequence assembler for very short reads"
HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
S="${WORKDIR}"/${MY_P}
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="doc openmp"
BDEPEND="
doc? ( virtual/latex-base )
openmp? (
|| (
sys-devel/gcc[openmp]
sys-devel/clang-runtime[openmp]
)
)
"
PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" )
pkg_pretend() {
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
}
pkg_setup() {
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
}
src_prepare() {
default
if ! use doc; then
sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
fi
elog "Upstream recommends using -O3 in CFLAGS"
echo
elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters"
elog "as described in the PDF manual, please set the variables by prepending VELVET_ in"
elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..."
elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge"
elog "the package. For example:"
elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
if [[ $(tc-getCC) =~ gcc ]]; then
local eopenmp=-fopenmp
elif [[ $(tc-getCC) =~ icc ]]; then
local eopenmp=-openmp
else
elog "Cannot detect compiler type so not setting openmp support"
fi
append-flags -fPIC ${eopenmp}
append-ldflags ${eopenmp}
tc-export CC
MAKE_XOPTS=(
CC="$(tc-getCC)"
CFLAGS="${CFLAGS}"
OPT="${CFLAGS}"
)
use openmp && MAKE_XOPTS+=( OPENMP=1 )
[[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} )
[[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} )
[[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} )
[[ ! -z "${VELVET_LONGSEQUENCES}" ]] && MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} )
}
src_compile() {
emake "${MAKE_XOPTS[@]}" -j1
emake "${MAKE_XOPTS[@]}" -j1 color
}
src_test() {
emake "${MAKE_XOPTS[@]}" -j1 test
}
src_install() {
dobin velvet{g,h,g_de,h_de}
insinto /usr/share/${PN}
doins -r contrib
dodoc Manual.pdf CREDITS.txt ChangeLog
}
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