add: rseqc and its dependencies

BioArchLinux/python-bx/PKGBUILD

@@ -0,0 +1,26 @@
+# Maintainer: sukanka <su975853527  at gmail>
+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
+}

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()

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'

BioArchLinux/python-pybigwig/PKGBUILD

@@ -0,0 +1,26 @@
+# Maintainer: Michael Schubert <mschu.dev at gmail>
+# Contributor: Clint Valentine <valentine.clint@gmail.com>
+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
+}

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()

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

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}}
 }

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()

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/