%global _empty_manifest_terminate_build 0 Name: python-sequana-pipetools Version: 0.12.4 Release: 1 Summary: A set of tools to help building or using Sequana pipelines License: new BSD URL: https://github.com/sequana/sequana_pipetools Source0: https://mirrors.aliyun.com/pypi/web/packages/ea/07/ea9aa3e08249828c1c2f9f8c6a66b20b5a0165a0867aa7875e9c40b6e5d4/sequana_pipetools-0.12.4.tar.gz BuildArch: noarch %description **sequana_pipetools** is a collection of tools that assists with the management of `Sequana `_ pipelines, which includes next-generation sequencing (NGS) pipelines like RNA-seq, variant calling, ChIP-seq, and others. The aim of this package is to simplify the deployment of `Sequana pipelines `_ by creatin a pure Python library that includse commonly used tools for different pipelines. Previously, the Sequana framework incorporated alll bioinformatics, Snakemake rules, pipelines, and pipeline management tools into a single library (Sequana) as illustrated in **Fig 1** below. **Figure 1** Old Sequana framework will all pipelines and Sequana library in the same place including pipetools (this library). Whenever changes were made to the Sequana library, a thorough check of the entire library was necessary, despite having 80% test coverage. Adding new pipelines also necessitated the addition of new dependencies, and the process was becoming increasingly complex. To mitigate this issue, we initially made all pipelines independent, as illustrated in **Fig. 2**. This way, pipeline changes could be made without updating Sequana and vice versa, which was a significant improvment. **Figure 2** v0.8 of Sequana moved the Snakemake pipelines in indepdendent repositories. A `cookie cutter `_ ease the creation of scuh pipelines However, certain tools, such as those used for user interface and input data sanity checks, were required by all pipelines, as depicted by the pipetools box in the figure. As new pipelines were being added every month, we aimed to make the pipelines and Sequana more modular. Consequently, we created a pure Python library known as **sequana_pipetools**, as shown in **Fig. 3**, to make the pipelines even more autonomous. **Figure 3** New Sequana framework. The library contains the core and bioinformatics tools and is now distinct from the pipelines. Additionally, the sequana_pipetools library supplies common tools to assist in the creaton and management of all pipelines, such as shared parser for options. Finally, we dropped the rules/ available in Sequana to build an independent package with a set of Snakemake wrappers. These wrappers are available on https://github.com/sequana/sequana-wrappers and have also the advantage of being tested through continuous integration. **Figure 3** New Sequana framework 2021. The library itself with the core, the bioinformatics tools is now fully independent of the pipelines. %package -n python3-sequana-pipetools Summary: A set of tools to help building or using Sequana pipelines Provides: python-sequana-pipetools BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-sequana-pipetools **sequana_pipetools** is a collection of tools that assists with the management of `Sequana `_ pipelines, which includes next-generation sequencing (NGS) pipelines like RNA-seq, variant calling, ChIP-seq, and others. The aim of this package is to simplify the deployment of `Sequana pipelines `_ by creatin a pure Python library that includse commonly used tools for different pipelines. Previously, the Sequana framework incorporated alll bioinformatics, Snakemake rules, pipelines, and pipeline management tools into a single library (Sequana) as illustrated in **Fig 1** below. **Figure 1** Old Sequana framework will all pipelines and Sequana library in the same place including pipetools (this library). Whenever changes were made to the Sequana library, a thorough check of the entire library was necessary, despite having 80% test coverage. Adding new pipelines also necessitated the addition of new dependencies, and the process was becoming increasingly complex. To mitigate this issue, we initially made all pipelines independent, as illustrated in **Fig. 2**. This way, pipeline changes could be made without updating Sequana and vice versa, which was a significant improvment. **Figure 2** v0.8 of Sequana moved the Snakemake pipelines in indepdendent repositories. A `cookie cutter `_ ease the creation of scuh pipelines However, certain tools, such as those used for user interface and input data sanity checks, were required by all pipelines, as depicted by the pipetools box in the figure. As new pipelines were being added every month, we aimed to make the pipelines and Sequana more modular. Consequently, we created a pure Python library known as **sequana_pipetools**, as shown in **Fig. 3**, to make the pipelines even more autonomous. **Figure 3** New Sequana framework. The library contains the core and bioinformatics tools and is now distinct from the pipelines. Additionally, the sequana_pipetools library supplies common tools to assist in the creaton and management of all pipelines, such as shared parser for options. Finally, we dropped the rules/ available in Sequana to build an independent package with a set of Snakemake wrappers. These wrappers are available on https://github.com/sequana/sequana-wrappers and have also the advantage of being tested through continuous integration. **Figure 3** New Sequana framework 2021. The library itself with the core, the bioinformatics tools is now fully independent of the pipelines. %package help Summary: Development documents and examples for sequana-pipetools Provides: python3-sequana-pipetools-doc %description help **sequana_pipetools** is a collection of tools that assists with the management of `Sequana `_ pipelines, which includes next-generation sequencing (NGS) pipelines like RNA-seq, variant calling, ChIP-seq, and others. The aim of this package is to simplify the deployment of `Sequana pipelines `_ by creatin a pure Python library that includse commonly used tools for different pipelines. Previously, the Sequana framework incorporated alll bioinformatics, Snakemake rules, pipelines, and pipeline management tools into a single library (Sequana) as illustrated in **Fig 1** below. **Figure 1** Old Sequana framework will all pipelines and Sequana library in the same place including pipetools (this library). Whenever changes were made to the Sequana library, a thorough check of the entire library was necessary, despite having 80% test coverage. Adding new pipelines also necessitated the addition of new dependencies, and the process was becoming increasingly complex. To mitigate this issue, we initially made all pipelines independent, as illustrated in **Fig. 2**. This way, pipeline changes could be made without updating Sequana and vice versa, which was a significant improvment. **Figure 2** v0.8 of Sequana moved the Snakemake pipelines in indepdendent repositories. A `cookie cutter `_ ease the creation of scuh pipelines However, certain tools, such as those used for user interface and input data sanity checks, were required by all pipelines, as depicted by the pipetools box in the figure. As new pipelines were being added every month, we aimed to make the pipelines and Sequana more modular. Consequently, we created a pure Python library known as **sequana_pipetools**, as shown in **Fig. 3**, to make the pipelines even more autonomous. **Figure 3** New Sequana framework. The library contains the core and bioinformatics tools and is now distinct from the pipelines. Additionally, the sequana_pipetools library supplies common tools to assist in the creaton and management of all pipelines, such as shared parser for options. Finally, we dropped the rules/ available in Sequana to build an independent package with a set of Snakemake wrappers. These wrappers are available on https://github.com/sequana/sequana-wrappers and have also the advantage of being tested through continuous integration. **Figure 3** New Sequana framework 2021. The library itself with the core, the bioinformatics tools is now fully independent of the pipelines. %prep %autosetup -n sequana_pipetools-0.12.4 %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-sequana-pipetools -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Tue Jun 20 2023 Python_Bot - 0.12.4-1 - Package Spec generated