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@@ -0,0 +1 @@ +/fuc-0.36.0.tar.gz diff --git a/python-fuc.spec b/python-fuc.spec new file mode 100644 index 0000000..f1e10da --- /dev/null +++ b/python-fuc.spec @@ -0,0 +1,149 @@ +%global _empty_manifest_terminate_build 0 +Name: python-fuc +Version: 0.36.0 +Release: 1 +Summary: Frequently used commands in bioinformatics +License: MIT +URL: https://github.com/sbslee/fuc +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/c3/c5/f5e7f40ce54db8de49d3092345dd9d5f05aba49a8f1c484bb8e5e78e8310/fuc-0.36.0.tar.gz +BuildArch: noarch + +Requires: python3-biopython +Requires: python3-lxml +Requires: python3-matplotlib +Requires: python3-matplotlib-venn +Requires: python3-numpy +Requires: python3-pandas +Requires: python3-pyranges +Requires: python3-pysam +Requires: python3-scipy +Requires: python3-seaborn +Requires: python3-statsmodels + +%description +The main goal of the fuc package (pronounced "eff-you-see") is to wrap some of the most **f**\ requently **u**\ sed **c**\ ommands in the field of bioinformatics into one place. +The package is written in Python, and supports both command line interface (CLI) and application programming interface (API) whose documentations are available at the `Read the Docs <https://sbslee-fuc.readthedocs.io/en/latest/>`_. +Currently, fuc can be used to analyze, summarize, visualize, and manipulate the following file formats: +- Sequence Alignment/Map (SAM) +- Binary Alignment/Map (BAM) +- CRAM +- Variant Call Format (VCF) +- Mutation Annotation Format (MAF) +- Browser Extensible Data (BED) +- FASTQ +- FASTA +- General Feature Format (GFF) +- Gene Transfer Format (GTF) +- delimiter-separated values format (e.g. comma-separated values or CSV format) +Additionally, fuc can be used to parse output data from the following programs: +- `Ensembl Variant Effect Predictor (VEP) <https://asia.ensembl.org/info/docs/tools/vep/index.html>`__ +- `SnpEff <http://pcingola.github.io/SnpEff/>`__ +- `bcl2fastq and bcl2fastq2 <https://sapac.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html>`__ +- `Kallisto <https://pachterlab.github.io/kallisto/>`__ +Your contributions (e.g. feature ideas, pull requests) are most welcome. +| Author: Seung-been "Steven" Lee +| Email: sbstevenlee@gmail.com +| License: MIT License + +%package -n python3-fuc +Summary: Frequently used commands in bioinformatics +Provides: python-fuc +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-fuc +The main goal of the fuc package (pronounced "eff-you-see") is to wrap some of the most **f**\ requently **u**\ sed **c**\ ommands in the field of bioinformatics into one place. +The package is written in Python, and supports both command line interface (CLI) and application programming interface (API) whose documentations are available at the `Read the Docs <https://sbslee-fuc.readthedocs.io/en/latest/>`_. +Currently, fuc can be used to analyze, summarize, visualize, and manipulate the following file formats: +- Sequence Alignment/Map (SAM) +- Binary Alignment/Map (BAM) +- CRAM +- Variant Call Format (VCF) +- Mutation Annotation Format (MAF) +- Browser Extensible Data (BED) +- FASTQ +- FASTA +- General Feature Format (GFF) +- Gene Transfer Format (GTF) +- delimiter-separated values format (e.g. comma-separated values or CSV format) +Additionally, fuc can be used to parse output data from the following programs: +- `Ensembl Variant Effect Predictor (VEP) <https://asia.ensembl.org/info/docs/tools/vep/index.html>`__ +- `SnpEff <http://pcingola.github.io/SnpEff/>`__ +- `bcl2fastq and bcl2fastq2 <https://sapac.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html>`__ +- `Kallisto <https://pachterlab.github.io/kallisto/>`__ +Your contributions (e.g. feature ideas, pull requests) are most welcome. +| Author: Seung-been "Steven" Lee +| Email: sbstevenlee@gmail.com +| License: MIT License + +%package help +Summary: Development documents and examples for fuc +Provides: python3-fuc-doc +%description help +The main goal of the fuc package (pronounced "eff-you-see") is to wrap some of the most **f**\ requently **u**\ sed **c**\ ommands in the field of bioinformatics into one place. +The package is written in Python, and supports both command line interface (CLI) and application programming interface (API) whose documentations are available at the `Read the Docs <https://sbslee-fuc.readthedocs.io/en/latest/>`_. +Currently, fuc can be used to analyze, summarize, visualize, and manipulate the following file formats: +- Sequence Alignment/Map (SAM) +- Binary Alignment/Map (BAM) +- CRAM +- Variant Call Format (VCF) +- Mutation Annotation Format (MAF) +- Browser Extensible Data (BED) +- FASTQ +- FASTA +- General Feature Format (GFF) +- Gene Transfer Format (GTF) +- delimiter-separated values format (e.g. comma-separated values or CSV format) +Additionally, fuc can be used to parse output data from the following programs: +- `Ensembl Variant Effect Predictor (VEP) <https://asia.ensembl.org/info/docs/tools/vep/index.html>`__ +- `SnpEff <http://pcingola.github.io/SnpEff/>`__ +- `bcl2fastq and bcl2fastq2 <https://sapac.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html>`__ +- `Kallisto <https://pachterlab.github.io/kallisto/>`__ +Your contributions (e.g. feature ideas, pull requests) are most welcome. +| Author: Seung-been "Steven" Lee +| Email: sbstevenlee@gmail.com +| License: MIT License + +%prep +%autosetup -n fuc-0.36.0 + +%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-fuc -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 0.36.0-1 +- Package Spec generated @@ -0,0 +1 @@ +579a09e67fddc054db75c07050a2cfa7 fuc-0.36.0.tar.gz |