From 5c83e3e4f9963ec92931ef6de348c5f764be1954 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Tue, 11 Apr 2023 20:08:09 +0000 Subject: automatic import of python-htseq --- python-htseq.spec | 388 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 388 insertions(+) create mode 100644 python-htseq.spec (limited to 'python-htseq.spec') diff --git a/python-htseq.spec b/python-htseq.spec new file mode 100644 index 0000000..4093fa2 --- /dev/null +++ b/python-htseq.spec @@ -0,0 +1,388 @@ +%global _empty_manifest_terminate_build 0 +Name: python-HTSeq +Version: 2.0.2 +Release: 1 +Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays +License: GPL3 +URL: https://github.com/htseq +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/de/13/cbeb753eb29d31bb252bc18443e79a3739bf5bd3dbc99e65fcf13db81be1/HTSeq-2.0.2.tar.gz +BuildArch: noarch + +Requires: python3-numpy +Requires: python3-pysam +Requires: python3-matplotlib +Requires: python3-scipy +Requires: python3-pytest +Requires: python3-pandas +Requires: python3-matplotlib + +%description +![CI](https://github.com/htseq/htseq/workflows/CI/badge.svg) +[![Documentation Status](https://readthedocs.org/projects/htseq/badge/?version=master)](https://htseq.readthedocs.io) + +# HTSeq +**DEVS**: https://github.com/htseq/htseq + +**DOCS**: https://htseq.readthedocs.io + +**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022). + +A Python library to facilitate programmatic analysis of data +from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq`` +is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq +and similar experiments. + +## Requirements + +To use ``HTSeq`` you need: + +- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped) +- ``numpy`` +- ``pysam`` + +To manipulate BigWig files, you also need: + +- ``pyBigWig`` + +To run the ``htseq-qa`` script, you also need: + +- ``matplotlib`` + +To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need: + +- ``mtx`` file: ``scipy`` +- ``h5ad`` file: ``anndata`` +- ``loom`` file: ``loompy`` + +Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We +would like to support **Windows** but currently lack the expertise to do so. If +you would like to take on the Windows release and maintenance, please open an +issue and we'll try to help. + +A source package which should not require ``Cython`` nor ``SWIG`` is also +provided on Pypi. + +To **develop** `HTSeq` you will **also** need: + +- ``Cython >=0.29.5`` +- ``SWIG >=3.0.8`` + +## Installation + +### PIP + +To install directly from PyPI: + +```bash +pip install HTSeq +``` + +To install a specific version: + +```bash +pip install 'HTSeq==2.0.0' +``` + +If this fails, please install all dependencies first: + +```bash +pip install matplotlib +pip install Cython +pip install pysam +pip install HTSeq +``` + +### setup.py (distutils/setuptools) + +Install the dependencies with your favourite tool (``pip``, ``conda``, +etc.). + +To install ``HTSeq`` itself, run: + +```bash +python setup.py build install +``` + +## Testing +To test locally, run + +```bash +./test.sh +``` + +To test `htseq-count` alone, run it with the `-o` option. + +A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts. + +## Authors +- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821)) +- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org +- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber + + + + +%package -n python3-HTSeq +Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays +Provides: python-HTSeq +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-HTSeq +![CI](https://github.com/htseq/htseq/workflows/CI/badge.svg) +[![Documentation Status](https://readthedocs.org/projects/htseq/badge/?version=master)](https://htseq.readthedocs.io) + +# HTSeq +**DEVS**: https://github.com/htseq/htseq + +**DOCS**: https://htseq.readthedocs.io + +**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022). + +A Python library to facilitate programmatic analysis of data +from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq`` +is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq +and similar experiments. + +## Requirements + +To use ``HTSeq`` you need: + +- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped) +- ``numpy`` +- ``pysam`` + +To manipulate BigWig files, you also need: + +- ``pyBigWig`` + +To run the ``htseq-qa`` script, you also need: + +- ``matplotlib`` + +To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need: + +- ``mtx`` file: ``scipy`` +- ``h5ad`` file: ``anndata`` +- ``loom`` file: ``loompy`` + +Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We +would like to support **Windows** but currently lack the expertise to do so. If +you would like to take on the Windows release and maintenance, please open an +issue and we'll try to help. + +A source package which should not require ``Cython`` nor ``SWIG`` is also +provided on Pypi. + +To **develop** `HTSeq` you will **also** need: + +- ``Cython >=0.29.5`` +- ``SWIG >=3.0.8`` + +## Installation + +### PIP + +To install directly from PyPI: + +```bash +pip install HTSeq +``` + +To install a specific version: + +```bash +pip install 'HTSeq==2.0.0' +``` + +If this fails, please install all dependencies first: + +```bash +pip install matplotlib +pip install Cython +pip install pysam +pip install HTSeq +``` + +### setup.py (distutils/setuptools) + +Install the dependencies with your favourite tool (``pip``, ``conda``, +etc.). + +To install ``HTSeq`` itself, run: + +```bash +python setup.py build install +``` + +## Testing +To test locally, run + +```bash +./test.sh +``` + +To test `htseq-count` alone, run it with the `-o` option. + +A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts. + +## Authors +- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821)) +- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org +- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber + + + + +%package help +Summary: Development documents and examples for HTSeq +Provides: python3-HTSeq-doc +%description help +![CI](https://github.com/htseq/htseq/workflows/CI/badge.svg) +[![Documentation Status](https://readthedocs.org/projects/htseq/badge/?version=master)](https://htseq.readthedocs.io) + +# HTSeq +**DEVS**: https://github.com/htseq/htseq + +**DOCS**: https://htseq.readthedocs.io + +**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022). + +A Python library to facilitate programmatic analysis of data +from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq`` +is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq +and similar experiments. + +## Requirements + +To use ``HTSeq`` you need: + +- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped) +- ``numpy`` +- ``pysam`` + +To manipulate BigWig files, you also need: + +- ``pyBigWig`` + +To run the ``htseq-qa`` script, you also need: + +- ``matplotlib`` + +To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need: + +- ``mtx`` file: ``scipy`` +- ``h5ad`` file: ``anndata`` +- ``loom`` file: ``loompy`` + +Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We +would like to support **Windows** but currently lack the expertise to do so. If +you would like to take on the Windows release and maintenance, please open an +issue and we'll try to help. + +A source package which should not require ``Cython`` nor ``SWIG`` is also +provided on Pypi. + +To **develop** `HTSeq` you will **also** need: + +- ``Cython >=0.29.5`` +- ``SWIG >=3.0.8`` + +## Installation + +### PIP + +To install directly from PyPI: + +```bash +pip install HTSeq +``` + +To install a specific version: + +```bash +pip install 'HTSeq==2.0.0' +``` + +If this fails, please install all dependencies first: + +```bash +pip install matplotlib +pip install Cython +pip install pysam +pip install HTSeq +``` + +### setup.py (distutils/setuptools) + +Install the dependencies with your favourite tool (``pip``, ``conda``, +etc.). + +To install ``HTSeq`` itself, run: + +```bash +python setup.py build install +``` + +## Testing +To test locally, run + +```bash +./test.sh +``` + +To test `htseq-count` alone, run it with the `-o` option. + +A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts. + +## Authors +- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821)) +- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org +- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber + + + + +%prep +%autosetup -n HTSeq-2.0.2 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-HTSeq -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot - 2.0.2-1 +- Package Spec generated -- cgit v1.2.3