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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit autotools flag-o-matic toolchain-funcs
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz
https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
RDEPEND="
!sci-biology/allpaths
!sci-biology/vaal"
DEPEND="
${RDEPEND}
dev-libs/boost:="
PATCHES=(
"${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch
"${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch
"${FILESDIR}"/${P}-gcc7.patch
)
pkg_pretend() {
# as of release 44849, GCC 4.7.0 (or higher) is required
# seems pre gcc-4.7 users must stay with:
# ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
if [[ ${MERGE_TYPE} != binary ]]; then
tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \
die "You need to use gcc >4.7"
fi
}
pkg_setup() {
if ! tc-has-openmp; then
ewarn "OpenMP is not available in your current selected compiler"
if tc-is-clang; then
ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp,"
ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\""
fi
die "need openmp capable compiler"
fi
}
src_prepare() {
default
eautoreconf
}
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