CGAT Apps

CGAT Apps is a collection of scripts to analyse high-throughput sequencing data.

After installation, use the cgat command to see how to use them.

More details coming soon, so stay tuned!

For questions, please open a discussion on the GitHub issue page.

Installation

Install using Conda

The preferred method to install CGAT Apps is using the installation script, which uses Conda.

Here are the steps:

# download installation script:
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-apps/master/install-CGAT-tools.sh

# see help:
bash install-CGAT-tools.sh

# install the development version (recommended, no production version yet):
bash install-CGAT-tools.sh --devel [--location </full/path/to/folder/without/trailing/slash>]

# the code is downloaded in zip format by default. If you want to get a git clone, use:
--git # for an HTTPS clone
--git-ssh # for a SSH clone (you need to be a cgat-developer contributor on GitHub to do this)

# enable the conda environment as requested by the installation script
# NB: you probably want to automate this by adding the instructions below to your .bashrc
source </full/path/to/folder/without/trailing/slash>/conda-install/etc/profile.d/conda.sh
conda activate base
conda activate cgat-a

# finally, please run the cgatflow 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