%global _empty_manifest_terminate_build 0 Name: python-hydra-genetics Version: 1.3.0 Release: 1 Summary: Helper tools for use with hydra-genetics pipelines. License: GPL-3 URL: https://github.com/hydra-genetics/tools Source0: https://mirrors.nju.edu.cn/pypi/web/packages/5e/04/3a92d9df734fc75a2ea670f9d74a2dcf45948657db2449871cac096ce3c9/hydra-genetics-1.3.0.tar.gz BuildArch: noarch %description # Hydra-genetics Command line interface to create new modules/pipelines or adding a new rule to an existing project. Provides libraries used to make it easier for people not used to pandas to extract information from samples and units dataframes. These dataframes are generated from [units.tsv](https://github.com/hydra-genetics/tools/blob/develop/hydra_genetics/pipeline-template/workflow/schemas/units.schema.yaml) and [samples.tsv](https://github.com/hydra-genetics/prealignment/blob/develop/workflow/schemas/samples.schema.yaml) files which are used as input. [![Lint and Test](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml/badge.svg?branch=develop)](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml) ![python](https://img.shields.io/badge/python-3.8-blue) ## Functions * create * reference Example of how to generate a new project ``` virtualenv -p python3.9 venv source venv/bin/activate pip install hydra-genetics hydra-genetics create-module -n snv -d "Collection of callers" -a "Patrik S" -e "p.s@mail.se" -g patrik -o snv # Create new smk file named "samtools.smk" with rule "samtools_rule2" hydra-genetics create-rule -c rule2 -t samtools -m snv -a test2 -e "test@test" # Add command to "samtools smk" file, rule name will be "samtools_rule3" hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test" # -t/--tool can be skipped for a single command tool, ex a script # this will create a smk file named "super_script.smk" with a rule "super_script" hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test" # Create input files hydra-genetics create-input-files -d path/dir1 -d path/dir2 # Create singularity cache # all container specified in config.yaml will be fetched hydra-genetics singularity create-singularity-files -o singularity_cache -c config.yaml ``` %package -n python3-hydra-genetics Summary: Helper tools for use with hydra-genetics pipelines. Provides: python-hydra-genetics BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-hydra-genetics # Hydra-genetics Command line interface to create new modules/pipelines or adding a new rule to an existing project. Provides libraries used to make it easier for people not used to pandas to extract information from samples and units dataframes. These dataframes are generated from [units.tsv](https://github.com/hydra-genetics/tools/blob/develop/hydra_genetics/pipeline-template/workflow/schemas/units.schema.yaml) and [samples.tsv](https://github.com/hydra-genetics/prealignment/blob/develop/workflow/schemas/samples.schema.yaml) files which are used as input. [![Lint and Test](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml/badge.svg?branch=develop)](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml) ![python](https://img.shields.io/badge/python-3.8-blue) ## Functions * create * reference Example of how to generate a new project ``` virtualenv -p python3.9 venv source venv/bin/activate pip install hydra-genetics hydra-genetics create-module -n snv -d "Collection of callers" -a "Patrik S" -e "p.s@mail.se" -g patrik -o snv # Create new smk file named "samtools.smk" with rule "samtools_rule2" hydra-genetics create-rule -c rule2 -t samtools -m snv -a test2 -e "test@test" # Add command to "samtools smk" file, rule name will be "samtools_rule3" hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test" # -t/--tool can be skipped for a single command tool, ex a script # this will create a smk file named "super_script.smk" with a rule "super_script" hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test" # Create input files hydra-genetics create-input-files -d path/dir1 -d path/dir2 # Create singularity cache # all container specified in config.yaml will be fetched hydra-genetics singularity create-singularity-files -o singularity_cache -c config.yaml ``` %package help Summary: Development documents and examples for hydra-genetics Provides: python3-hydra-genetics-doc %description help # Hydra-genetics Command line interface to create new modules/pipelines or adding a new rule to an existing project. Provides libraries used to make it easier for people not used to pandas to extract information from samples and units dataframes. These dataframes are generated from [units.tsv](https://github.com/hydra-genetics/tools/blob/develop/hydra_genetics/pipeline-template/workflow/schemas/units.schema.yaml) and [samples.tsv](https://github.com/hydra-genetics/prealignment/blob/develop/workflow/schemas/samples.schema.yaml) files which are used as input. [![Lint and Test](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml/badge.svg?branch=develop)](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml) ![python](https://img.shields.io/badge/python-3.8-blue) ## Functions * create * reference Example of how to generate a new project ``` virtualenv -p python3.9 venv source venv/bin/activate pip install hydra-genetics hydra-genetics create-module -n snv -d "Collection of callers" -a "Patrik S" -e "p.s@mail.se" -g patrik -o snv # Create new smk file named "samtools.smk" with rule "samtools_rule2" hydra-genetics create-rule -c rule2 -t samtools -m snv -a test2 -e "test@test" # Add command to "samtools smk" file, rule name will be "samtools_rule3" hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test" # -t/--tool can be skipped for a single command tool, ex a script # this will create a smk file named "super_script.smk" with a rule "super_script" hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test" # Create input files hydra-genetics create-input-files -d path/dir1 -d path/dir2 # Create singularity cache # all container specified in config.yaml will be fetched hydra-genetics singularity create-singularity-files -o singularity_cache -c config.yaml ``` %prep %autosetup -n hydra-genetics-1.3.0 %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-hydra-genetics -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Mon May 15 2023 Python_Bot - 1.3.0-1 - Package Spec generated