commit: 19fb6fba9514187c9c16052b5f93866d53858b55 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sat Jan 15 13:05:12 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sat Jan 15 13:05:12 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=19fb6fba
sci-biology/minimap2: version bump 2.24, add python flag Closes: https://github.com/gentoo/sci/issues/1125 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/minimap2/minimap2-2.23.ebuild | 57 ---------------------------- sci-biology/minimap2/minimap2-2.24.ebuild | 63 +++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+), 57 deletions(-) diff --git a/sci-biology/minimap2/minimap2-2.23.ebuild b/sci-biology/minimap2/minimap2-2.23.ebuild deleted file mode 100644 index eb8d98991..000000000 --- a/sci-biology/minimap2/minimap2-2.23.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1" -HOMEPAGE="https://github.com/lh3/minimap2"; -SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="+static" - -DEPEND="sys-libs/zlib" -RDEPEND="${DEPEND}" -BDEPEND="" - -src_prepare(){ - sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die - eapply_user -} - -# Minimap2 requires SSE2 instructions on x86 CPUs or NEON on ARM CPUs. It is -# possible to add non-SIMD support, but it would make minimap2 slower by -# several times. -# -# If you see compilation errors, try `make sse2only=1` -# to disable SSE4 code, which will make minimap2 slightly slower. -# -# Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To -# compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To -# compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1 -# aarch64=1`. -# -# Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting -# implementation to the different SIMD instruction sets. To compile using SIMDe, -# use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde` -# with the ARM related command lines given above. - -# This repository also provides Python bindings to a subset of C APIs. File -# [python/README.rst](python/README.rst) gives the full documentation; -# [python/minimap2.py](python/minimap2.py) shows an example. This Python -# extension, mappy, is also [available from PyPI][mappypypi] via `pip install -# mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`. - -src_install(){ - dobin "${PN}" - insinto /usr/include - doins minimap.h mmpriv.h - dolib.a libminimap2.a - insinto /usr/share/"${PN}"/examples - doins example.c - doman minimap2.1 - dodoc README.md NEWS.md FAQ.md -} diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild new file mode 100644 index 000000000..f39de8ead --- /dev/null +++ b/sci-biology/minimap2/minimap2-2.24.ebuild @@ -0,0 +1,63 @@ +# Copyright 2021-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) +DISTUTILS_OPTIONAL=1 +inherit distutils-r1 + +DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1" +HOMEPAGE="https://github.com/lh3/minimap2"; +SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="python cpu_flags_x86_sse4_1" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="sys-libs/zlib + python? ( + ${PYTHON_DEPS} + )" +RDEPEND="${DEPEND}" +BDEPEND="python? ( dev-python/cython[${PYTHON_USEDEP}] )" + +src_prepare(){ + sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die + if ! use cpu_flags_x86_sse4_1; then + sed -i -e "/extra_compile_args.append('-msse4.1')/d" setup.py || die + fi + if use python; then + distutils-r1_src_prepare + fi + default +} + +src_configure() { + if use python; then + distutils-r1_src_configure + fi + default +} + +src_compile() { + if use python; then + distutils-r1_src_compile + fi + default +} + +src_install() { + if use python; then + distutils-r1_src_install + fi + dobin "${PN}" + insinto /usr/include + doins minimap.h mmpriv.h + insinto /usr/share/"${PN}"/examples + doins example.c + doman minimap2.1 + einstalldocs +}
