diff --git a/BioArchLinux/python-bx/PKGBUILD b/BioArchLinux/python-bx/PKGBUILD new file mode 100644 index 0000000000..974b8b3bb5 --- /dev/null +++ b/BioArchLinux/python-bx/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: sukanka +pkgname=python-bx +_pkgname=bx-python +pkgver=0.8.13 +pkgrel=0 +pkgdesc="Tools for manipulating biological data, particularly multiple sequence alignments" +arch=('x86_64') +url="https://github.com/bxlab/bx-python" +license=('MIT') +depends=('lzo' 'python' 'python-numpy') +makedepends=('python-setuptools' 'cython' ) +provides=('bx-python') +options=(!emptydirs) +source=($_pkgname-$pkgver.tar.gz::$url/archive/v$pkgver.tar.gz) +sha256sums=('38597646e52ae183a03a598759ce152af91199a32c5a82c3be2b0f7ead0e1880') + +build(){ + cd "$srcdir"/$_pkgname-$pkgver + python setup.py build +} + +package() { + cd $_pkgname-$pkgver + python setup.py install --root="$pkgdir" --optimize=1 --skip-build + install -Dm644 LICENSE "$pkgdir"/usr/share/licenses/$pkgname/LICENSE +} diff --git a/BioArchLinux/python-bx/lilac.py b/BioArchLinux/python-bx/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/BioArchLinux/python-bx/lilac.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/python-bx/lilac.yaml b/BioArchLinux/python-bx/lilac.yaml new file mode 100644 index 0000000000..1c7dce5d13 --- /dev/null +++ b/BioArchLinux/python-bx/lilac.yaml @@ -0,0 +1,9 @@ +build_prefix: extra-x86_64 +maintainers: + - github: sukanka + email: su975853527@gmail.com +update_on: + - source: github + github: bxlab/bx-python + use_latest_release: true + prefix: 'v' diff --git a/BioArchLinux/python-pybigwig/PKGBUILD b/BioArchLinux/python-pybigwig/PKGBUILD new file mode 100644 index 0000000000..3c168dee14 --- /dev/null +++ b/BioArchLinux/python-pybigwig/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Michael Schubert +# Contributor: Clint Valentine +pkgname=python-pybigwig +_pkgname=pyBigWig +pkgver=0.3.18 +pkgrel=0 +pkgdesc="A Python extension for quick access to bigWig and bigBed files" +arch=('any') +url="https://github.com/deeptools/pyBigWig" +license=('MIT') +depends=('curl' 'python-numpy') +makedepends=('python-setuptools') +options=(!emptydirs) +source=($_pkgname-$pkgver.tar.gz::$url/archive/$pkgver.tar.gz) +sha256sums=('552564d8ce8720a8ae70ed5e5534617fb0cab306b666468d1c61b6d389b8a10c') + +build(){ + cd "$srcdir"/$_pkgname-$pkgver + python setup.py build +} + +package() { + cd $_pkgname-$pkgver + python setup.py install --root="$pkgdir" --optimize=1 --skip-build + install -Dm644 LICENSE.txt "$pkgdir"/usr/share/licenses/$pkgname/LICENSE.txt +} diff --git a/BioArchLinux/python-pybigwig/lilac.py b/BioArchLinux/python-pybigwig/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/BioArchLinux/python-pybigwig/lilac.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/python-pybigwig/lilac.yaml b/BioArchLinux/python-pybigwig/lilac.yaml new file mode 100644 index 0000000000..d2b13f77fe --- /dev/null +++ b/BioArchLinux/python-pybigwig/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: + - github: sukanka + email: su975853527@gmail.com +update_on: + - source: github + github: deeptools/pyBigWig + use_latest_release: true diff --git a/prepare/rseqc/PKGBUILD b/BioArchLinux/rseqc/PKGBUILD similarity index 79% rename from prepare/rseqc/PKGBUILD rename to BioArchLinux/rseqc/PKGBUILD index 02b6e64e89..17d0c088fe 100644 --- a/prepare/rseqc/PKGBUILD +++ b/BioArchLinux/rseqc/PKGBUILD @@ -2,7 +2,7 @@ pkgname=rseqc pkgver=4.0.0 -pkgrel=1 +pkgrel=0 pkgdesc="An RNA-seq Quality Control Package" arch=('any') url="http://rseqc.sourceforge.net/" @@ -22,4 +22,8 @@ build() { package() { cd "$srcdir/RSeQC-${pkgver}" python setup.py install --root="$pkgdir" --optimize=1 + + # these files owned by python-bx. + rm -rf ${pkgdir}/usr/lib/python3.10/site-packages/\ + {psyco_full.py,__pycache__/psyco_full.cpython-310{.opt-1.pyc,.pyc}} } diff --git a/BioArchLinux/rseqc/lilac.py b/BioArchLinux/rseqc/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/BioArchLinux/rseqc/lilac.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/rseqc/lilac.yaml b/BioArchLinux/rseqc/lilac.yaml new file mode 100644 index 0000000000..73cad07b9c --- /dev/null +++ b/BioArchLinux/rseqc/lilac.yaml @@ -0,0 +1,11 @@ +build_prefix: extra-x86_64 +maintainers: + - github: sukanka + email: su975853527@gmail.com +repo_depends: + - python-pybigwig + - python-bx +update_on: + - source: regex + regex: 'RSeQC v(\d+.\d+.\d+)' + url: http://rseqc.sourceforge.net/