summarylogtreecommitdiffstats
path: root/PKGBUILD
diff options
context:
space:
mode:
Diffstat (limited to 'PKGBUILD')
-rw-r--r--PKGBUILD92
1 files changed, 26 insertions, 66 deletions
diff --git a/PKGBUILD b/PKGBUILD
index e5e220bbffb..a69066195bd 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,72 +1,32 @@
# Maintainer: Clint Valentine <valentine.clint@gmail.com>
-
-_name=pybedtools
-pkgbase='python-pybedtools'
-pkgname=('python-pybedtools' 'python2-pybedtools')
-pkgver=0.7.10
-pkgrel=4
-pkgdesc="Python wrapper for the bioinformatics genomic arithmetic tool bedtools"
+_base=pybedtools
+pkgname=python-${_base}
+pkgver=0.8.2
+pkgrel=1
+pkgdesc="Wrapper around BEDTools for bioinformatics work"
arch=('any')
-url="https://pypi.python.org/pypi/pybedtools"
-license=('GPL2')
-makedepends=(
- 'python' 'python-setuptools' 'cython'
- 'python2' 'python2-setuptools' 'cython2')
-options=(!emptydirs)
-source=("${pkgname}"-"${pkgver}".tar.gz::https://pypi.python.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz)
-sha256sums=('518a2311bd33f29cf2ee8fc1a028dda8c8e380c9fc83fcb0fbaa206933174b50')
-
-prepare() {
- cp -a "${_name}"-"${pkgver}"{,-py2}
-}
-
-build(){
- cd "${srcdir}"/"${_name}"-"${pkgver}"
+url="https://github.com/daler/${_base}"
+license=(GPL2)
+depends=(bedtools python-pandas python-pysam)
+makedepends=(cython)
+optdepends=(
+ 'htslib: for working with SAM/BAM/CRAM files'
+ 'python-matplotlib: for plotting genomic intervals'
+ 'ucsc-kent-genome-tools: for bedgraph to bigwig conversions')
+provides=('python-pyvcf')
+conflicts=('python-pyvcf')
+# options=(!emptydirs)
+source=(https://pypi.org/packages/source/${_base::1}/${_base}/${_base}-${pkgver}.tar.gz)
+sha512sums=('82af299ec90ce3c80922c82146d0fe26897c243d08d0abc452c667f7183bc89c0f806427fb6691f730c4ddfe8f93e04f59d64b4911297bc30dcbf83a6716cd6d')
+
+build() {
+ cd "${_base}-${pkgver}"
python setup.py build
-
- cd "${srcdir}"/"${_name}"-"${pkgver}"-py2
- python2 setup.py build
}
-package_python2-pybedtools() {
- 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')
-
- 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 "${script%.*py}")2.py
- done
-}
-
-package_python-pybedtools() {
- depends=(
- 'bedtools'
- 'python'
- 'python-numpy'
- 'python-pandas'
- 'python-pysam'
- 'python-six')
- optdepends=(
- 'htslib: for working with SAM/BAM/CRAM files'
- 'python-matplotlib: for plotting genomic intervals'
- 'ucsc-kent-genome-tools: for bedgraph to bigwig conversions')
-
- cd "${_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 "${_base}-${pkgver}"
+ 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}"
}