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# 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"
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/"${_name}".git)
sha256sums=('SKIP')
pkgver() {
cd "${_name}"-"${pkgver}"
git describe --long | sed 's/\([^-]*-g\)/r\1/;s/-/./g' | sed s'/v//'
}
prepare() {
cp -a "${_name}"-"${pkgver}"{,-py2}
}
build(){
cd "${srcdir}"/"${_name}"-"${pkgver}"
python setup.py build
cd "${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
}
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