diff options
Diffstat (limited to 'PKGBUILD')
| -rw-r--r-- | PKGBUILD | 94 |
1 files changed, 25 insertions, 69 deletions
@@ -1,81 +1,37 @@ # Maintainer: Clint Valentine <valentine.clint@gmail.com> - -_name=pybedtools -pkgbase='python-pybedtools-git' -pkgname=('python-pybedtools-git' 'python2-pybedtools-git') -pkgver=0.7.10.r25.g9ab3ff6 -pkgrel=2 -pkgdesc="Python wrapper for the bioinformatics genomic arithmetic tool bedtools" +_base=pybedtools +pkgname=python-${_base}-git +pkgver=0.8.0.r138.gffe0d4b +pkgrel=1 +pkgdesc="Wrapper around BEDTools for bioinformatics work" arch=('any') -url="https://pypi.python.org/pypi/pybedtools" -license=('GPL2') -makedepends=( - 'python' 'python-setuptools' 'cython' - 'python2' 'python2-setuptools' 'cython2') -options=(!emptydirs) -source=("${_name}"-"${pkgver}"::git+https://github.com/daler/"${_name}".git) +url="https://github.com/daler/${_base}" +license=(GPL2) +depends=(bedtools python-pandas python-pysam) +makedepends=(cython git) +optdepends=( + 'htslib: for working with SAM/BAM/CRAM files' + 'python-matplotlib: for plotting genomic intervals' + 'ucsc-kent-genome-tools: for bedgraph to bigwig conversions') +provides=('python-pyvcf') +conflicts=('python-pyvcf') +# options=(!emptydirs) +source=(git+${url}.git) sha256sums=('SKIP') pkgver() { - cd "${_name}"-"${pkgver}" + cd "${_base}" git describe --long | sed 's/\([^-]*-g\)/r\1/;s/-/./g' | sed s'/v//' } -prepare() { - cp -a "${_name}"-"${pkgver}"{,-py2} -} - -build(){ - cd "${srcdir}"/"${_name}"-"${pkgver}" +build() { + cd "${_base}" python setup.py build - - cd "${srcdir}"/"${_name}"-"${pkgver}"-py2 - python2 setup.py build -} - -package_python2-pybedtools-git() { - depends=( - 'bedtools' - 'python2' - 'python2-numpy' - 'python2-pandas' - 'python2-pysam' - 'python2-six') - optdepends=( - 'htslib: for working with SAM/BAM/CRAM files' - 'python2-matplotlib: for plotting genomic intervals' - 'ucsc-kent-genome-tools: for bedgraph to bigwig conversions') - provides=('python2-pyvcf') - conflicts=('python2-pyvcf') - - cd "${_name}"-"${pkgver}"-py2 - python2 setup.py install --root="${pkgdir}"/ --optimize=1 --skip-build - install -Dm644 LICENSE.txt "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE.txt - - sed 's/python/python2/g' "${pkgdir}"/usr/bin/pybedtools - mv "${pkgdir}"/usr/bin/pybedtools "${pkgdir}"/usr/bin/pybedtools2 - - for script in "${pkgdir}"/usr/bin/*.py;do - mv "${script}" "${pkgdir}"/usr/bin/$(basename "${script%.*py}")2.py - done } -package_python-pybedtools-git() { - depends=( - 'bedtools' - 'python' - 'python-numpy' - 'python-pandas' - 'python-pysam' - 'python-six') - optdepends=( - 'htslib: for working with SAM/BAM/CRAM files' - 'python-matplotlib: for plotting genomic intervals' - 'ucsc-kent-genome-tools: for bedgraph to bigwig conversions') - provides=('python-pyvcf') - conflicts=('python-pyvcf') - - cd "${_name}"-"${pkgver}" - python setup.py install --root="${pkgdir}"/ --optimize=1 --skip-build - install -Dm644 LICENSE.txt "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE.txt +package() { + cd "${_base}" + export PYTHONHASHSEED=0 + PYTHONPYCACHEPREFIX="${PWD}/.cache/cpython/" python setup.py install --prefix=/usr --root="${pkgdir}" --optimize=1 --skip-build + install -Dm 644 LICENSE.txt -t "${pkgdir}/usr/share/licenses/${pkgname}" } |