From 6924612269bf345b9a17c7cc3936348be677f0ae Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Mon, 15 May 2023 06:43:42 +0000 Subject: automatic import of python-cooler --- .gitignore | 1 + python-cooler.spec | 528 +++++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 530 insertions(+) create mode 100644 python-cooler.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..0159a54 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/cooler-0.9.1.tar.gz diff --git a/python-cooler.spec b/python-cooler.spec new file mode 100644 index 0000000..a10feef --- /dev/null +++ b/python-cooler.spec @@ -0,0 +1,528 @@ +%global _empty_manifest_terminate_build 0 +Name: python-cooler +Version: 0.9.1 +Release: 1 +Summary: Sparse binary format for genomic interaction matrices. +License: BSD-3-Clause +URL: https://pypi.org/project/cooler/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/80/65/96c623d5ee993ebd51d643bd877621161a3e6a0ebbca8029693311833633/cooler-0.9.1.tar.gz +BuildArch: noarch + +Requires: python3-numpy +Requires: python3-scipy +Requires: python3-pandas +Requires: python3-h5py +Requires: python3-click +Requires: python3-cytoolz +Requires: python3-multiprocess +Requires: python3-pyfaidx +Requires: python3-asciitree +Requires: python3-pyyaml +Requires: python3-simplejson +Requires: python3-biopython +Requires: python3-dask[array,dataframe] +Requires: python3-ipytree +Requires: python3-ipywidgets +Requires: python3-matplotlib +Requires: python3-pypairix +Requires: python3-psutil +Requires: python3-pysam +Requires: python3-Sphinx +Requires: python3-sphinx-rtd-theme +Requires: python3-m2r +Requires: python3-numpydoc +Requires: python3-recommonmark +Requires: python3-coverage[toml] +Requires: python3-flake8 +Requires: python3-flake8-pyproject +Requires: python3-isort +Requires: python3-pytest +Requires: python3-pytest-cov + +%description +# Cooler + +Cooler + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Latest Release + + latest release pypi + + + latest release bioconda + +
License + + license + + +
Build Status + + build status + +
Pre-commit Status + + pre-commit status + +
Docs Status + + + +
Coverage + + coverage + +
Downloads + + pypi downloads + + + bioconda downloads + +
Citation + + paper doi + + + zenodo doi + +
Community + + slack + +
+ +## A cool place to store your Hi-C + +Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. + +The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files. + +To get started: + +- [Install](#Installation) cooler +- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder). +- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`. +- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index). + +### Installation + +Install from PyPI using pip. +```sh +$ pip install cooler +``` + +If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel. +```sh +$ conda install -c conda-forge -c bioconda cooler +``` + +### Citing + +Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540). + +```bibtex +@article{cooler2020, + author = {Abdennur, Nezar and Mirny, Leonid A}, + title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}", + journal={Bioinformatics}, + volume={36}, + number={1}, + pages={311--316}, + year={2020}, + doi = {10.1093/bioinformatics/btz540}, + url = {https://doi.org/10.1093/bioinformatics/btz540}, +} +``` + +### Contributing + +Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md). + + +### Related projects + +- Process Hi-C data with [distiller](https://github.com/open2c/distiller)! +- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)! +- Visualize your cooler data with [HiGlass](http://higlass.io)! + + +%package -n python3-cooler +Summary: Sparse binary format for genomic interaction matrices. +Provides: python-cooler +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-cooler +# Cooler + +Cooler + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Latest Release + + latest release pypi + + + latest release bioconda + +
License + + license + + +
Build Status + + build status + +
Pre-commit Status + + pre-commit status + +
Docs Status + + + +
Coverage + + coverage + +
Downloads + + pypi downloads + + + bioconda downloads + +
Citation + + paper doi + + + zenodo doi + +
Community + + slack + +
+ +## A cool place to store your Hi-C + +Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. + +The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files. + +To get started: + +- [Install](#Installation) cooler +- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder). +- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`. +- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index). + +### Installation + +Install from PyPI using pip. +```sh +$ pip install cooler +``` + +If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel. +```sh +$ conda install -c conda-forge -c bioconda cooler +``` + +### Citing + +Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540). + +```bibtex +@article{cooler2020, + author = {Abdennur, Nezar and Mirny, Leonid A}, + title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}", + journal={Bioinformatics}, + volume={36}, + number={1}, + pages={311--316}, + year={2020}, + doi = {10.1093/bioinformatics/btz540}, + url = {https://doi.org/10.1093/bioinformatics/btz540}, +} +``` + +### Contributing + +Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md). + + +### Related projects + +- Process Hi-C data with [distiller](https://github.com/open2c/distiller)! +- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)! +- Visualize your cooler data with [HiGlass](http://higlass.io)! + + +%package help +Summary: Development documents and examples for cooler +Provides: python3-cooler-doc +%description help +# Cooler + +Cooler + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Latest Release + + latest release pypi + + + latest release bioconda + +
License + + license + + +
Build Status + + build status + +
Pre-commit Status + + pre-commit status + +
Docs Status + + + +
Coverage + + coverage + +
Downloads + + pypi downloads + + + bioconda downloads + +
Citation + + paper doi + + + zenodo doi + +
Community + + slack + +
+ +## A cool place to store your Hi-C + +Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. + +The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files. + +To get started: + +- [Install](#Installation) cooler +- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder). +- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`. +- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index). + +### Installation + +Install from PyPI using pip. +```sh +$ pip install cooler +``` + +If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel. +```sh +$ conda install -c conda-forge -c bioconda cooler +``` + +### Citing + +Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540). + +```bibtex +@article{cooler2020, + author = {Abdennur, Nezar and Mirny, Leonid A}, + title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}", + journal={Bioinformatics}, + volume={36}, + number={1}, + pages={311--316}, + year={2020}, + doi = {10.1093/bioinformatics/btz540}, + url = {https://doi.org/10.1093/bioinformatics/btz540}, +} +``` + +### Contributing + +Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md). + + +### Related projects + +- Process Hi-C data with [distiller](https://github.com/open2c/distiller)! +- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)! +- Visualize your cooler data with [HiGlass](http://higlass.io)! + + +%prep +%autosetup -n cooler-0.9.1 + +%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-cooler -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot - 0.9.1-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..8e999fc --- /dev/null +++ b/sources @@ -0,0 +1 @@ +eea7594f756d8350b4cd241e9a41e218 cooler-0.9.1.tar.gz -- cgit v1.2.3