| Name | cgat JSON |
| Version |
0.7.10
JSON |
| download |
| home_page | None |
| Summary | cgat : the Computational Genomics Analysis Toolkit |
| upload_time | 2024-11-30 10:28:25 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT |
| keywords |
computational
genomics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<p align="left">
<a href='https://cgat-apps.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/cgat-apps/badge/?version=latest' alt='Documentation Status' /></a>
<a href='https://github.com/cgat-developers/cgat-apps/actions/workflows/cgatapps_python.yml'>
<img src='https://github.com/cgat-developers/cgat-apps/actions/workflows/cgatapps_python.yml/badge.svg' alt='Github Action status' /></a>
<a href="https://twitter.com/cgat_oxford?lang=en", alt="Twitter followers">
<img src="https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter" /></a>
<a href="https://twitter.com/cgat_oxford?lang=en", alt="Twitter followers">
<img src="https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter" /></a>
</p>
CGAT Apps
=========
CGAT Apps is a collection of scripts to aid the analysis of high-throughput sequencing data.
After installation, use the ``cgat`` command to see how to use them.
Documentation
=============
We are attempting to improve our documentation. However, our current documentation
can be found [here](https://cgat-apps.readthedocs.io/en/latest/)
For questions, please open a discussion on the GitHub
[issue page](https://github.com/cgat-developers/cgat-apps/issues)
Installation
============
Conda Installation
------------------
The preferred method to install CGAT Apps is using the installation script, which uses
[mamba](https://github.com/mamba-org/mamba), the fast C implementation of [Conda](https://conda.io).
To install cgat-apps using mamba::
mamba install -c conda-forge -c bioconda cgat-apps
Developers: try the installation script
---------------------------------------
Here are the steps::
# Install conda and mamba according the the documentation. Next
# install the conda packages for cgat-apps to work
conda env create -f conda/environments/cgat-apps.yml
# enable the conda environment
conda activate cgat-a
# Install the development version of cgat-apps
python setup.py develop
# finally, please run the cgat command-line tool to check the installation:
cgat --help
The installation script will put everything under the specified location. The aim is to provide a portable
installation that does not interfere with the existing software. As a result, you will get a conda environment
working with CGAT Apps which can be enabled on demand according to your needs.
Usage
=====
Run the ``cgat --help`` command to see what scripts are available and how to use them.
For example, to strip sequence and quality information from a bam_ file, type::
cgat bam2bam --strip=sequence < in.bam > out.bam
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"description": "\n<p align=\"left\">\n<a href='https://cgat-apps.readthedocs.io/en/latest/?badge=latest'>\n <img src='https://readthedocs.org/projects/cgat-apps/badge/?version=latest' alt='Documentation Status' /></a>\n <a href='https://github.com/cgat-developers/cgat-apps/actions/workflows/cgatapps_python.yml'>\n <img src='https://github.com/cgat-developers/cgat-apps/actions/workflows/cgatapps_python.yml/badge.svg' alt='Github Action status' /></a>\n <a href=\"https://twitter.com/cgat_oxford?lang=en\", alt=\"Twitter followers\">\n <img src=\"https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter\" /></a>\n <a href=\"https://twitter.com/cgat_oxford?lang=en\", alt=\"Twitter followers\">\n\t<img src=\"https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter\" /></a>\n</p>\n\nCGAT Apps\n=========\n\nCGAT Apps is a collection of scripts to aid the analysis of high-throughput sequencing data.\n\nAfter installation, use the ``cgat`` command to see how to use them.\n\nDocumentation\n=============\n\nWe are attempting to improve our documentation. However, our current documentation\ncan be found [here](https://cgat-apps.readthedocs.io/en/latest/)\n\nFor questions, please open a discussion on the GitHub\n[issue page](https://github.com/cgat-developers/cgat-apps/issues)\n\nInstallation\n============\n\nConda Installation\n------------------\nThe preferred method to install CGAT Apps is using the installation script, which uses\n[mamba](https://github.com/mamba-org/mamba), the fast C implementation of [Conda](https://conda.io).\n\nTo install cgat-apps using mamba::\n\n mamba install -c conda-forge -c bioconda cgat-apps\n\nDevelopers: try the installation script\n---------------------------------------\n\nHere are the steps::\n\n # Install conda and mamba according the the documentation. Next\n # install the conda packages for cgat-apps to work\n conda env create -f conda/environments/cgat-apps.yml\n\n # enable the conda environment\n conda activate cgat-a\n\n # Install the development version of cgat-apps\n python setup.py develop\n\n # finally, please run the cgat command-line tool to check the installation:\n cgat --help\n\nThe installation script will put everything under the specified location. The aim is to provide a portable\ninstallation that does not interfere with the existing software. As a result, you will get a conda environment\nworking with CGAT Apps which can be enabled on demand according to your needs.\n\nUsage\n=====\n\nRun the ``cgat --help`` command to see what scripts are available and how to use them.\nFor example, to strip sequence and quality information from a bam_ file, type::\n\n cgat bam2bam --strip=sequence < in.bam > out.bam\n",
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