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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit git-r3
DESCRIPTION="Probabilistic framework for structural variant discovery"
HOMEPAGE="https://github.com/arq5x/lumpy-sv"
EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git"
LICENSE="MIT"
SLOT="0"
KEYWORDS=""
IUSE=""
# contains bundled htslib
CDEPEND="dev-util/cmake"
DEPEND=""
RDEPEND="${DEPEND}"
src_install(){
cat > "${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/*
dodoc README.md
insinto /usr/share/lumpy-sv/scripts/bamkit
cd scripts/bamkit || die
doins *.py sectosupp
newdoc README.md README_bamkit.md
}
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