automatic import of python-staphb-toolkitopeneuler20.03

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+/staphb_toolkit-2.0.1.tar.gz
diff --git a/python-staphb-toolkit.spec b/python-staphb-toolkit.spec
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+%global _empty_manifest_terminate_build 0
+Name:		python-staphb-toolkit
+Version:	2.0.1
+Release:	1
+Summary:	A ToolKit of commonly used Public Health Bioinformatics Tools
+License:	GNU General Public License v3 (GPLv3)
+URL:		https://github.com/StaPH-B/staphb_toolkit
+Source0:	https://mirrors.aliyun.com/pypi/web/packages/f0/3f/c068851ec9c5b1778abe0a706dae33c21174dbc7926b1a37d7187acefe2a/staphb_toolkit-2.0.1.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-spython
+Requires:	python3-psutil
+Requires:	python3-docker
+Requires:	python3-pexpect
+Requires:	python3-pyfiglet
+Requires:	python3-rich
+
+%description
+# StaPH-B ToolKit
+![Latest Release](https://img.shields.io/github/v/release/StaPH-B/staphb_toolkit)  
+[![Build Status](https://travis-ci.org/StaPH-B/staphb_toolkit.svg?branch=master)](https://travis-ci.org/StaPH-B/staphb_toolkit)  
+
+A python library designed to make bioinformatics piplines and applications more accessible to public health scientists.
+
+### [staphb.org/staphb_toolkit/](https://staphb.org/staphb_toolkit/)
+
+## Summary
+The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the [StaPH-B Docker Images](https://github.com/StaPH-B/docker-builds) to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
+
+## Motivation
+Public health bioinformatics is dependent on open-source software that require carefully curated computational environments and various software dependencies. Setting up and maintaining such environments requires a skill set and expertise absent in most public health laboratories. The [StaPH-B Docker Images](https://github.com/StaPH-B/docker-builds) have helped generate reproducible computational environments through the use of containerization. However, access to these images is dependent on a working understanding of containerization, which is not available in most laboratories. The ToolKit addresses this issue through the handling of the StaPH-B docker images allowing users to interact with bioinformatis programs without needing to interact directly with mounted file systems and running containers. The goal of the Toolkit is it increase usability while mirroring the functionality of a locally-installed tool.
+
+## Installing and Usage
+The ToolKit requires **either** singularity or docker, Python 3.7 or greater, and Java version 8 or later.
+The documentation for installing the dependencies can be found here: [https://staph-b.github.io/staphb_toolkit/install](https://staph-b.github.io/staphb_toolkit/install).  
+The ToolKit itself can be installed using pip or by cloning the repository from git:
+
+To install using pip:
+```
+$ pip install staphb_toolkit
+```
+
+To install using git:
+```
+$ git clone https://github.com/StaPH-B/staphb_toolkit.git
+$ cd staphb_toolkit/packaging/
+$ ./setup.py install
+```
+
+Test the pipeline with the following command and ensure you see the same usage output:  
+```
+$ staphb-tk
+     _______.___________.    ___      .______    __    __         .______   
+    /       |           |   /   \     |   _  \  |  |  |  |        |   _  \  
+   |   (----`---|  |----`  /  ^  \    |  |_)  | |  |__|  |  ______|  |_)  |
+    \   \       |  |      /  /_\  \   |   ___/  |   __   | |______|   _  <  
+.----)   |      |  |     /  _____  \  |  |      |  |  |  |        |  |_)  |
+|_______/       |__|    /__/     \__\ | _|      |__|  |__|        |______/  
+
+.___________.  ______     ______    __       __  ___  __  .___________.
+|           | /  __  \   /  __  \  |  |     |  |/  / |  | |           |
+`---|  |----`|  |  |  | |  |  |  | |  |     |  '  /  |  | `---|  |----`
+    |  |     |  |  |  | |  |  |  | |  |     |    <   |  |     |  |     
+    |  |     |  `--'  | |  `--'  | |  `----.|  .  \  |  |     |  |     
+    |__|      \______/   \______/  |_______||__|\__\ |__|     |__|     
+
+
+StaPH-B ToolKit
+Version: 2.0.0
+usage: staphb-tk [optional arguments] <application/workflow> [application/workflow arguments]
+
+optional arguments:
+-h, --help            show this help message and exit
+-l, --list_tools      List all tools in the toolkit.
+-w, --list_workflows  List all workflows in the toolkit.
+-wv <version>, --workflow_version <version>
+                   Version of tool or workflow to run. Default: latest
+-c <config_file>, --configuration <config_file>
+                   Specify a custom workflow configuration file.
+-gc, --get_configuration
+                   Get the configuration file for the specified workflow.
+                   Note: You may need to specify a version for the
+                   workflow using -wv to get the correct configuration
+                   file.
+-nv [<version>], --nextflow_version [<version>]
+                   Get or set the version of nextflow.
+--update              Check for and install a ToolKit update.
+--auto_update         Toggle automatic ToolKit updates. Default is off.
+
+application or workflow name:
+<application/workflow>
+
+```
+
+
+%package -n python3-staphb-toolkit
+Summary:	A ToolKit of commonly used Public Health Bioinformatics Tools
+Provides:	python-staphb-toolkit
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-staphb-toolkit
+# StaPH-B ToolKit
+![Latest Release](https://img.shields.io/github/v/release/StaPH-B/staphb_toolkit)  
+[![Build Status](https://travis-ci.org/StaPH-B/staphb_toolkit.svg?branch=master)](https://travis-ci.org/StaPH-B/staphb_toolkit)  
+
+A python library designed to make bioinformatics piplines and applications more accessible to public health scientists.
+
+### [staphb.org/staphb_toolkit/](https://staphb.org/staphb_toolkit/)
+
+## Summary
+The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the [StaPH-B Docker Images](https://github.com/StaPH-B/docker-builds) to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
+
+## Motivation
+Public health bioinformatics is dependent on open-source software that require carefully curated computational environments and various software dependencies. Setting up and maintaining such environments requires a skill set and expertise absent in most public health laboratories. The [StaPH-B Docker Images](https://github.com/StaPH-B/docker-builds) have helped generate reproducible computational environments through the use of containerization. However, access to these images is dependent on a working understanding of containerization, which is not available in most laboratories. The ToolKit addresses this issue through the handling of the StaPH-B docker images allowing users to interact with bioinformatis programs without needing to interact directly with mounted file systems and running containers. The goal of the Toolkit is it increase usability while mirroring the functionality of a locally-installed tool.
+
+## Installing and Usage
+The ToolKit requires **either** singularity or docker, Python 3.7 or greater, and Java version 8 or later.
+The documentation for installing the dependencies can be found here: [https://staph-b.github.io/staphb_toolkit/install](https://staph-b.github.io/staphb_toolkit/install).  
+The ToolKit itself can be installed using pip or by cloning the repository from git:
+
+To install using pip:
+```
+$ pip install staphb_toolkit
+```
+
+To install using git:
+```
+$ git clone https://github.com/StaPH-B/staphb_toolkit.git
+$ cd staphb_toolkit/packaging/
+$ ./setup.py install
+```
+
+Test the pipeline with the following command and ensure you see the same usage output:  
+```
+$ staphb-tk
+     _______.___________.    ___      .______    __    __         .______   
+    /       |           |   /   \     |   _  \  |  |  |  |        |   _  \  
+   |   (----`---|  |----`  /  ^  \    |  |_)  | |  |__|  |  ______|  |_)  |
+    \   \       |  |      /  /_\  \   |   ___/  |   __   | |______|   _  <  
+.----)   |      |  |     /  _____  \  |  |      |  |  |  |        |  |_)  |
+|_______/       |__|    /__/     \__\ | _|      |__|  |__|        |______/  
+
+.___________.  ______     ______    __       __  ___  __  .___________.
+|           | /  __  \   /  __  \  |  |     |  |/  / |  | |           |
+`---|  |----`|  |  |  | |  |  |  | |  |     |  '  /  |  | `---|  |----`
+    |  |     |  |  |  | |  |  |  | |  |     |    <   |  |     |  |     
+    |  |     |  `--'  | |  `--'  | |  `----.|  .  \  |  |     |  |     
+    |__|      \______/   \______/  |_______||__|\__\ |__|     |__|     
+
+
+StaPH-B ToolKit
+Version: 2.0.0
+usage: staphb-tk [optional arguments] <application/workflow> [application/workflow arguments]
+
+optional arguments:
+-h, --help            show this help message and exit
+-l, --list_tools      List all tools in the toolkit.
+-w, --list_workflows  List all workflows in the toolkit.
+-wv <version>, --workflow_version <version>
+                   Version of tool or workflow to run. Default: latest
+-c <config_file>, --configuration <config_file>
+                   Specify a custom workflow configuration file.
+-gc, --get_configuration
+                   Get the configuration file for the specified workflow.
+                   Note: You may need to specify a version for the
+                   workflow using -wv to get the correct configuration
+                   file.
+-nv [<version>], --nextflow_version [<version>]
+                   Get or set the version of nextflow.
+--update              Check for and install a ToolKit update.
+--auto_update         Toggle automatic ToolKit updates. Default is off.
+
+application or workflow name:
+<application/workflow>
+
+```
+
+
+%package help
+Summary:	Development documents and examples for staphb-toolkit
+Provides:	python3-staphb-toolkit-doc
+%description help
+# StaPH-B ToolKit
+![Latest Release](https://img.shields.io/github/v/release/StaPH-B/staphb_toolkit)  
+[![Build Status](https://travis-ci.org/StaPH-B/staphb_toolkit.svg?branch=master)](https://travis-ci.org/StaPH-B/staphb_toolkit)  
+
+A python library designed to make bioinformatics piplines and applications more accessible to public health scientists.
+
+### [staphb.org/staphb_toolkit/](https://staphb.org/staphb_toolkit/)
+
+## Summary
+The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the [StaPH-B Docker Images](https://github.com/StaPH-B/docker-builds) to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
+
+## Motivation
+Public health bioinformatics is dependent on open-source software that require carefully curated computational environments and various software dependencies. Setting up and maintaining such environments requires a skill set and expertise absent in most public health laboratories. The [StaPH-B Docker Images](https://github.com/StaPH-B/docker-builds) have helped generate reproducible computational environments through the use of containerization. However, access to these images is dependent on a working understanding of containerization, which is not available in most laboratories. The ToolKit addresses this issue through the handling of the StaPH-B docker images allowing users to interact with bioinformatis programs without needing to interact directly with mounted file systems and running containers. The goal of the Toolkit is it increase usability while mirroring the functionality of a locally-installed tool.
+
+## Installing and Usage
+The ToolKit requires **either** singularity or docker, Python 3.7 or greater, and Java version 8 or later.
+The documentation for installing the dependencies can be found here: [https://staph-b.github.io/staphb_toolkit/install](https://staph-b.github.io/staphb_toolkit/install).  
+The ToolKit itself can be installed using pip or by cloning the repository from git:
+
+To install using pip:
+```
+$ pip install staphb_toolkit
+```
+
+To install using git:
+```
+$ git clone https://github.com/StaPH-B/staphb_toolkit.git
+$ cd staphb_toolkit/packaging/
+$ ./setup.py install
+```
+
+Test the pipeline with the following command and ensure you see the same usage output:  
+```
+$ staphb-tk
+     _______.___________.    ___      .______    __    __         .______   
+    /       |           |   /   \     |   _  \  |  |  |  |        |   _  \  
+   |   (----`---|  |----`  /  ^  \    |  |_)  | |  |__|  |  ______|  |_)  |
+    \   \       |  |      /  /_\  \   |   ___/  |   __   | |______|   _  <  
+.----)   |      |  |     /  _____  \  |  |      |  |  |  |        |  |_)  |
+|_______/       |__|    /__/     \__\ | _|      |__|  |__|        |______/  
+
+.___________.  ______     ______    __       __  ___  __  .___________.
+|           | /  __  \   /  __  \  |  |     |  |/  / |  | |           |
+`---|  |----`|  |  |  | |  |  |  | |  |     |  '  /  |  | `---|  |----`
+    |  |     |  |  |  | |  |  |  | |  |     |    <   |  |     |  |     
+    |  |     |  `--'  | |  `--'  | |  `----.|  .  \  |  |     |  |     
+    |__|      \______/   \______/  |_______||__|\__\ |__|     |__|     
+
+
+StaPH-B ToolKit
+Version: 2.0.0
+usage: staphb-tk [optional arguments] <application/workflow> [application/workflow arguments]
+
+optional arguments:
+-h, --help            show this help message and exit
+-l, --list_tools      List all tools in the toolkit.
+-w, --list_workflows  List all workflows in the toolkit.
+-wv <version>, --workflow_version <version>
+                   Version of tool or workflow to run. Default: latest
+-c <config_file>, --configuration <config_file>
+                   Specify a custom workflow configuration file.
+-gc, --get_configuration
+                   Get the configuration file for the specified workflow.
+                   Note: You may need to specify a version for the
+                   workflow using -wv to get the correct configuration
+                   file.
+-nv [<version>], --nextflow_version [<version>]
+                   Get or set the version of nextflow.
+--update              Check for and install a ToolKit update.
+--auto_update         Toggle automatic ToolKit updates. Default is off.
+
+application or workflow name:
+<application/workflow>
+
+```
+
+
+%prep
+%autosetup -n staphb_toolkit-2.0.1
+
+%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-staphb-toolkit -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 2.0.1-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..afe76a3
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+253b8646a205ac95053222a1edaaf8d4  staphb_toolkit-2.0.1.tar.gz