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.

We are attempting to improve our documentation. However, our current documentation can be found here

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

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

To install cgat-apps using conda::

conda install -c conda-forge -c bioconda cgat-apps

Alternatively, installation can be performed using our install script that will automate the process for you.

Here are the steps::

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

    # see help:
    bash install.sh

    # install the development version (recommended, no production version yet):
    bash install.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.

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

cgat-core samtools