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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit toolchain-funcs
DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
HOMEPAGE="https://github.com/alexdobin/STAR"
SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
RDEPEND="sci-libs/htslib:="
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
PATCHES=(
"${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch
"${FILESDIR}"/${PN}-2.7.10a-missing-include.patch
)
DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
pkg_pretend() {
[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
}
pkg_setup() {
[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
}
src_prepare() {
default
# remove bundled htslib
rm -r source/htslib || die
}
src_configure() {
tc-export CC CXX PKG_CONFIG
}
src_compile() {
emake -C source STAR
}
src_install() {
dobin source/STAR
einstalldocs
}
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