mirror of
https://github.com/gentoo-mirror/gentoo.git
synced 2026-01-06 02:17:34 -08:00
f135183356
Update done using: ``` git grep -l sys-libs/zlib dev-* | xargs sed -i -e s@sys-libs/zlib@virtual/zlib@g git diff --name-only | xargs copybump git diff --name-only | xargs grep -l PYTHON_COMPAT | xargs gpy-impl -@dead pkgcheck scan --commits -c SourcingCheck,VisibilityCheck --exit error ``` Signed-off-by: Michał Górny <mgorny@gentoo.org>
69 lines
1.5 KiB
Bash
69 lines
1.5 KiB
Bash
# Copyright 1999-2025 Gentoo Authors
|
|
# Distributed under the terms of the GNU General Public License v2
|
|
|
|
EAPI=8
|
|
|
|
inherit cmake flag-o-matic
|
|
|
|
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:=
|
|
virtual/zlib:=
|
|
hdf5? ( sci-libs/hdf5:= )"
|
|
DEPEND="
|
|
${RDEPEND}
|
|
test? (
|
|
>=dev-cpp/catch-3:0
|
|
sci-libs/hdf5
|
|
)"
|
|
BDEPEND="virtual/pkgconfig"
|
|
|
|
PATCHES=(
|
|
"${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
|
|
|
|
# This randomly hardcodes a particular std, which unfortunately is too old for catch2.
|
|
sed -i '/CMAKE_CXX_STANDARD/d' CMakeLists.txt || die
|
|
append-cxxflags -std=c++14
|
|
}
|
|
|
|
src_configure() {
|
|
local mycmakeargs=(
|
|
-DUSE_HDF5=$(usex hdf5)
|
|
-DBUILD_TESTING=$(usex test)
|
|
# convenience library only
|
|
-DBUILD_SHARED_LIBS=OFF
|
|
)
|
|
cmake_src_configure
|
|
}
|