mirror of
https://github.com/BioArchLinux/Packages.git
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78 lines
2.9 KiB
Bash
78 lines
2.9 KiB
Bash
# Maintainer:Bipin Kumar <kbipinkumar@pm.me>
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pkgbase=abpoa
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pkgname=('abpoa' 'pyabpoa')
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pkgname=abpoa
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pkgdesc="SIMD-based C library for fast partial order alignment. https://dx.doi.org/10.1093/bioinformatics/btaa963"
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_name=abPOA
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pkgver=1.5.3
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pkgrel=2
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arch=(x86_64)
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url="https://github.com/yangao07/abPOA"
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license=('MIT')
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makedepends=('cmake' 'git' 'python-build' 'quilt' 'simde' 'python'
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'python-installer' 'python-setuptools'
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'python-wheel'
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'cython')
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source=("${pkgbase}-${pkgver}.tar.gz::https://github.com/yangao07/abPOA/archive/refs/tags/v${pkgver}.tar.gz"
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"baseline.patch"
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"series"
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"buildflags.patch"
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"simde.patch"
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"relax-cython-dep.patch"
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)
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b2sums=('6e4a9d4e6ccb6aa6a08aca438dd9eb99551a3de8c0539d237db432557d521edd05d8ff8c9841d27d82a5541e4b32aa5559d18dd2e673a489cc81ad56801b6ada'
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'ca47e595ff4d1b27e72ccb8ca900ba1524a23444198be4e9a05b8f49688832553d8e035f391f359d5fb3324ba23178ba5ac280069c46121f0c17e6d6050c66e2'
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'6ef4e3d5f8a37bc103ca2b720bf4a064825b25382d2cb6d99edfeb5388fda821190dd0ebc35e0ab3e1507e4c27f6815f843419bcfbb9c017594165d377c49a02'
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'531591beb6430dabb045167a96d901af2fc4945a88b17ca7ba369115bf6314b7d4aa1830a3ca9748ed0cf8a5b5e1a48389ac830bc1a1e5276be1b22ad1b8e11e'
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'59ebf7e79f80bae90dea9b03e649ac21ea31a2759d0ca340ac5060927c758e3c09327d9074db3ad0abab16d2f15293a3dc611c67388d60b94aad61dfd4a12b99'
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'd7b5054c4a4092e345bf1d893645eb3a3516faf2b0f76f13f022c01ae3deb6b7d4f871ded08d97d6a44372354aeebbfa8cfcc87cec145eb04514c336fc302e27')
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prepare() {
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# adapt patches from debian to make use SIMDe from Archlinux repo
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mkdir -p ${_name}-${pkgver}/patches
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cp series ${_name}-${pkgver}/patches
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cp *.patch ${_name}-${pkgver}/patches
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cd ${_name}-${pkgver}/patches
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quilt push -a
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}
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build() {
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cd ${_name}-${pkgver}
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cmake -B build \
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-DCMAKE_BUILD_TYPE='None' \
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-DCMAKE_INSTALL_PREFIX='/usr' \
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-DCMAKE_SKIP_INSTALL_RPATH=YES \
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-DCMAKE_INSTALL_INCLUDEDIR='include/${pkgname}' \
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-Wno-dev
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cmake --build build
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python -m build --wheel --no-isolation
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}
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check() {
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cd ${_name}-${pkgver}/build
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./bin/abpoa ../test_data/seq.fa > cons.fa
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}
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package_abpoa() {
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pkgdesc="SIMD-based C library for fast partial order alignment. https://dx.doi.org/10.1093/bioinformatics/btaa963"
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depends=('glibc'
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'zlib'
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'graphviz')
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optdepends=('pyabpoa: python bindings for abpoa')
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cd ${_name}-${pkgver}
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install -d 755 ${pkgdir}/usr
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DESTDIR="$pkgdir" cmake --install build
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install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE
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rm -rf "$pkgdir"/usr/include/simde
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}
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package_pyabpoa() {
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depends=('glibc'
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'zlib'
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'python'
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'graphviz')
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pkgdesc="python bindings for abpoa"
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provides=('pyabpoa')
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cd ${_name}-${pkgver}
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python -m installer --destdir="$pkgdir" dist/*.whl
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install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE
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}
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