MAVIS (Mini) Tutorial

This tutorial is based on the data included in the tests folder of MAVIS. The data files are very small and this tutorial is really only intended for testing a MAVIS install. The data here is simulated and results are not representative of the typical events you would see reported from MAVIS. For a more complete tutorial with actual fusion gene examples, please see the full tutorial.

The first step is to clone or download a zip of the MAVIS repository (https://github.com/bcgsc/mavis). You will need the tests directory. The tag you check out should correspond to the MAVIS version you have installed

git clone https://github.com/bcgsc/mavis.git
git checkout <VERSION_TAG>
mv mavis/tests .
mv mavis/Snakefile .
rm -r mavis

Now you should have a folder called tests in your current directory. Since this is a trivial example, it can easily be run locally. However in order to run the snakemake file you will need to have the config validation module mavis_config installed which has minimal dependencies.

pip install mavis_config

Now you are ready to run MAVIS. This can be done in a single command using snakemake.

snakemake -j 1 --configfile=tests/mini-tutorial.config.json -s Snakefile

Which will run the mini tutorial version and output files into a folder called output_dir in the current directory