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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit cmake
DESCRIPTION="Near-optimal RNA-Seq quantification"
HOMEPAGE="http://pachterlab.github.io/kallisto/"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
else
SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
fi
LICENSE="BSD"
SLOT="0"
IUSE="hdf5 test"
RESTRICT="!test? ( test )"
RDEPEND="
sci-libs/htslib:=
sys-libs/zlib:=
hdf5? ( sci-libs/hdf5:= )"
DEPEND="
${RDEPEND}
test? (
dev-cpp/catch:0
sci-libs/hdf5
)"
BDEPEND="virtual/pkgconfig"
PATCHES=(
"${FILESDIR}"/${P}-cmake.patch
"${FILESDIR}"/${P}-htslib.patch
"${FILESDIR}"/${P}-catch2.patch
"${FILESDIR}"/${P}-gcc11.patch
)
src_prepare() {
cmake_src_prepare
# bundled catch2
rm -r ext || die
# bundled htslib structs
rm src/kseq.h || die
# the test suite is cheesy and relies on a
# specific builddir nesting structure.
sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \
-i unit_tests/test_kmerhashtable.cpp || die
}
src_configure() {
local mycmakeargs=(
-DUSE_HDF5=$(usex hdf5)
-DBUILD_TESTING=$(usex test)
# convenience library only
-DBUILD_SHARED_LIBS=OFF
)
cmake_src_configure
}
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