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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
DESCRIPTION="Probabilistic framework for structural variant discovery"
HOMEPAGE="https://github.com/arq5x/lumpy-sv"
SRC_URI="https://github.com/arq5x/lumpy-sv/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
DEPEND="sci-libs/htslib"
RDEPEND="${DEPEND}"
src_prepare() {
default
# do not build bundled htslib, link to system lib
sed -i -e 's/lumpy_filter: htslib/lumpy_filter:/g' Makefile || die
sed -i -e 's/-I..\/..\/lib\/htslib\///' -e 's/..\/..\/lib\/htslib\/libhts.a/-lhts/g' src/filter/Makefile || die
}
src_install(){
cat > "${T}"/99lumpy-sv <<- EOF
LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv
PAIREND_DISTRO=${EPREFIX}/usr/share/lumpy-sv/scripts/pairend_distro.py
BAMGROUPREADS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py
BAMFILTERRG=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py
BAMLIBS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py
EOF
doenvd "${T}"/99lumpy-sv
rm -f bin/lumpyexpress.config
dobin bin/*
insinto /usr/share/lumpy-sv/scripts
for f in lumpyexpress lumpyexpress.config; do
rm scripts/"$f" || die
done
doins scripts/*
einstalldocs
}