add: taco, ucsc-genome-browser

BioArchLinux/taco/PKGBUILD

@@ -0,0 +1,18 @@
+# Maintainer: sukanka <su975853527 at gmail dot com>
+
+pkgname=taco
+pkgver=0.7.3
+pkgrel=1
+pkgdesc="Multi-sample transcriptome assembly from RNA-Seq"
+arch=('x86_64')
+url="https://tacorna.github.io/"
+depends=('zlib')
+license=('MIT')
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/tacorna/taco/releases/download/v${pkgver}/taco-v${pkgver}.Linux_x86_64.tar.gz")
+sha256sums=('fe00b16a3657aadec25d9dc5491971056f35a71dda0bfcb36656902236964588')
+
+
+package() {
+	cd "$srcdir/${pkgname}-v${pkgver}.Linux_x86_64/"
+	install -Dm755 taco_refcomp taco_run -t ${pkgdir}/usr/bin
+}

BioArchLinux/taco/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/taco/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: sukanka
+  email: su975853527@gmail.com
+
+update_on:
+- source: github
+  github: tacorna/taco
+  use_latest_release: true
+  prefix: 'v'

BioArchLinux/ucsc-genome-browser/PKGBUILD

@@ -0,0 +1,21 @@
+# Maintainer: sukanka <su975853527 at gmail dot com>
+pkgname=ucsc-genome-browser
+pkgver=433
+pkgrel=1
+pkgdesc="An RNA-seq Quality Control Package"
+arch=('x86_64')
+url="https://github.com/ucscGenomeBrowser/kent"
+license=('custom' 'MIT')
+depends=('perl' 'python' 'curl')
+makedepends=('rsync')
+prepare(){
+	rsync -aP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ ${srcdir}/${pkgname}-${pkgver}
+	cd ${srcdir}/${pkgname}-${pkgver}
+	# fix  for python3
+	sed -i 's|#!/usr/bin/env python2.7|#!/usr/bin/env python|' expMatrixToBarchartBed bedJoinTabOffset.py
+}
+
+package() {
+	cd ${srcdir}/${pkgname}-${pkgver}
+	find . -type f -executable -print0 | xargs -0 install -Dm755 -t ${pkgdir}/usr/bin/
+}

BioArchLinux/ucsc-genome-browser/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/ucsc-genome-browser/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: sukanka
+  email: su975853527@gmail.com
+update_on:
+- regex: 'v\d+_base'
+  source: regex
+  url: https://github.com/ucscGenomeBrowser/kent/tags

prepare/taco/PKGBUILD

@@ -1,28 +0,0 @@
-# Maintainer: sukanka <su975853527 at gmail dot com>
-
-pkgname=taco
-pkgver=0.7.3
-pkgrel=1
-pkgdesc="Multi-sample transcriptome assembly from RNA-Seq"
-arch=('x86_64')
-url="https://tacorna.github.io/"
-license=('MIT')
-depends=('python' 'cython' 'python-numpy' 'python-pandas')
-makedepends=('python-setuptools' 'python-pip')
-source=("${pkgname}-${pkgver}.tar.gz::https://github.com/tacorna/taco/archive/refs/tags/v${pkgver}.tar.gz")
-sha256sums=('441499883e92462f14050f9e011c0c225950ab679c6bfa7ead5e4cb592b1f69b')
-
-prepare(){
-	cd "$srcdir/${pkgname}-${pkgver}"
-	sed -i 's|cythonize(cython_extensions)|cythonize(cython_extensions, compiler_directives={"language_level": 3})|' setup.py
-}
-
-build() {
-	cd "$srcdir/${pkgname}-${pkgver}"
-	python setup.py build
-}
-
-package() {
-	cd "$srcdir/${pkgname}-${pkgver}"
-	python setup.py install --root="$pkgdir" --optimize=1
-}

prepare/ucsc-genome-browser/PKGBUILD

@@ -1,30 +0,0 @@
-# Maintainer: sukanka <su975853527 at gmail dot com>
-pkgname=ucsc-genome-browser
-pkgver=434_preview2
-pkgrel=1
-pkgdesc="An RNA-seq Quality Control Package"
-arch=('x86_64')
-url="https://github.com/ucscGenomeBrowser/kent"
-license=('custom')
-depends=('python' 'python-django')
-makedepends=('python-setuptools' 'python-pip' 'python')
-source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ucscGenomeBrowser/kent/archive/refs/tags/v${pkgver}.tar.gz")
-sha256sums=('b8918077405653b859ec8fc3ac33c464afc82500b9f892b03a7fb8ba17c6534f')
-
-
-
-build() {
-	cd "$srcdir/kent-${pkgver}"
-	2to3 --output-dir=python3 -W -n --no-diffs python
-	cd python3/lib
-	python setup.py build
-	cd "$srcdir/kent-${pkgver}"/src
-	make
-}
-
-package() {
-	cd "$srcdir/kent-${pkgver}"/python3/lib
-	python setup.py install --root="$pkgdir" --optimize=1
-	cd "$srcdir/kent-${pkgver}"/src
-	make install DESTDIR="$pkgdir"
-}