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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
[](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
[](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
[](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
|
