The VAtools suite is written for Linux and Mac OS X. If you are using Windows you will need to set up a Linux environment, for example by setting up a virtual machine.

VAtools requires Python 3.5 or above. Before running any installation steps, check the Python version installed on your system:

python -V

If you don’t have Python 3 installed, we recommend using Conda to emulate a Python 3. environment. We’ve encountered problems with users that already have Python 2.x installed when they also try to install Python 3. The defaults will not be set correctly in that case. If you already have Python 2.x installed we strongly recommmend using Conda instead of installing Python 3 locally.

Once you have set up your Python 3 environment correctly you can use pip to install VAtools. Make sure you have pip installed. pip is generally included in python distributions, but may need to be upgraded before use. See the instructions for installing or upgrading pip.

After you have pip installed, type the following command on your Terminal:

pip install vatools

You can check that the vatools package has been installed under the default environment by running this command:

pip show vatools

pip will fetch and install VAtools and its dependencies for you. After installing, each tool of the VAtools package is available in its own command line tree directly from the Terminal.

If you have an old version of the vatools package installed you might want to consider upgrading to the latest version:

pip install vatools --upgrade


A Docker container for VAtools is available on DockerHub using the griffithlab/vatools repo.