From e454696782e7a8e70647d4372eee741598be78f5 Mon Sep 17 00:00:00 2001 From: sukanka Date: Sun, 17 Jul 2022 11:22:53 +0800 Subject: [PATCH] add: taco, ucsc-genome-browser --- BioArchLinux/taco/PKGBUILD | 18 +++++++++++++ BioArchLinux/taco/lilac.py | 10 +++++++ BioArchLinux/taco/lilac.yaml | 10 +++++++ BioArchLinux/ucsc-genome-browser/PKGBUILD | 21 +++++++++++++++ BioArchLinux/ucsc-genome-browser/lilac.py | 10 +++++++ BioArchLinux/ucsc-genome-browser/lilac.yaml | 8 ++++++ prepare/taco/PKGBUILD | 28 ------------------- prepare/ucsc-genome-browser/PKGBUILD | 30 --------------------- 8 files changed, 77 insertions(+), 58 deletions(-) create mode 100644 BioArchLinux/taco/PKGBUILD create mode 100644 BioArchLinux/taco/lilac.py create mode 100644 BioArchLinux/taco/lilac.yaml create mode 100644 BioArchLinux/ucsc-genome-browser/PKGBUILD create mode 100644 BioArchLinux/ucsc-genome-browser/lilac.py create mode 100644 BioArchLinux/ucsc-genome-browser/lilac.yaml delete mode 100644 prepare/taco/PKGBUILD delete mode 100644 prepare/ucsc-genome-browser/PKGBUILD diff --git a/BioArchLinux/taco/PKGBUILD b/BioArchLinux/taco/PKGBUILD new file mode 100644 index 0000000000..af15e9b453 --- /dev/null +++ b/BioArchLinux/taco/PKGBUILD @@ -0,0 +1,18 @@ +# Maintainer: sukanka + +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 +} diff --git a/BioArchLinux/taco/lilac.py b/BioArchLinux/taco/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/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() diff --git a/BioArchLinux/taco/lilac.yaml b/BioArchLinux/taco/lilac.yaml new file mode 100644 index 0000000000..70c05bd3be --- /dev/null +++ b/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' diff --git a/BioArchLinux/ucsc-genome-browser/PKGBUILD b/BioArchLinux/ucsc-genome-browser/PKGBUILD new file mode 100644 index 0000000000..2e04c5710a --- /dev/null +++ b/BioArchLinux/ucsc-genome-browser/PKGBUILD @@ -0,0 +1,21 @@ +# Maintainer: sukanka +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 ${pkgdir}/usr/bin/ +} diff --git a/BioArchLinux/ucsc-genome-browser/lilac.py b/BioArchLinux/ucsc-genome-browser/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/BioArchLinux/ucsc-genome-browser/lilac.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/ucsc-genome-browser/lilac.yaml b/BioArchLinux/ucsc-genome-browser/lilac.yaml new file mode 100644 index 0000000000..59b06510d8 --- /dev/null +++ b/BioArchLinux/ucsc-genome-browser/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: +- github: sukanka + email: su975853527@gmail.com +update_on: +- regex: 'v\d+_base' + source: regex + url: https://github.com/ucscGenomeBrowser/kent/tags diff --git a/prepare/taco/PKGBUILD b/prepare/taco/PKGBUILD deleted file mode 100644 index 44f88e9551..0000000000 --- a/prepare/taco/PKGBUILD +++ /dev/null @@ -1,28 +0,0 @@ -# Maintainer: sukanka - -pkgname=taco -pkgver=0.7.3 -pkgrel=1 -pkgdesc="Multi-sample transcriptome assembly from RNA-Seq" -arch=('x86_64') -url="https://tacorna.github.io/" -license=('MIT') -depends=('python' 'cython' 'python-numpy' 'python-pandas') -makedepends=('python-setuptools' 'python-pip') -source=("${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 -} diff --git a/prepare/ucsc-genome-browser/PKGBUILD b/prepare/ucsc-genome-browser/PKGBUILD deleted file mode 100644 index 38e66bd094..0000000000 --- a/prepare/ucsc-genome-browser/PKGBUILD +++ /dev/null @@ -1,30 +0,0 @@ -# Maintainer: sukanka -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" -}