From f79667b00d9865832b858232f87c5cb52991bc35 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Mon, 15 May 2023 05:07:12 +0000 Subject: automatic import of python-hydra-genetics --- .gitignore | 1 + python-hydra-genetics.spec | 186 +++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 188 insertions(+) create mode 100644 python-hydra-genetics.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..63d3015 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/hydra-genetics-1.3.0.tar.gz diff --git a/python-hydra-genetics.spec b/python-hydra-genetics.spec new file mode 100644 index 0000000..9bd163e --- /dev/null +++ b/python-hydra-genetics.spec @@ -0,0 +1,186 @@ +%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 diff --git a/sources b/sources new file mode 100644 index 0000000..f8423aa --- /dev/null +++ b/sources @@ -0,0 +1 @@ +2bb495b55e1d49942f1217bcc65e77ff hydra-genetics-1.3.0.tar.gz -- cgit v1.2.3