Installation instructions

The section below describes how to install the cgat-apps. We distinguish between two different installation types: production and development. The former refers to the released version of our tools, which can be installed using pip or conda, and is the recommended installation for users. The latter refers to the installation of the development version of the apps, which can be used to make changes to our code base.

Please note that we can not test our code on all systems and configurations out there so please bear with us.

Quick installation

Install using Conda

Conda Installation

The preferred method to install CGAT Apps is using the installation script, which uses mamba, the fast C implementation of conda.

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 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.

Install using pip

You can also use pip to install the CGAT scripts. To go down this route, please type:

pip install cgat

However, cgat-apps depends on numerous other python packages which themselves might require manual intervention.