walter

Snakemake workflow for running multiple methdemons in a cluster environment (or locally, but why...?). Much like methdemon being a for of demon_model, walter draws heavily from warlock.

Set-up

To clone the repository, run

git clone https://github.com/vesmanojlovic/walter --recursive
cd walter

The --recursive flag is required to include the methdemon submodule. Next, compile methdemon

cd resources/methdemon/
# edit the Makefile to contain your boost library path
make all
cd ../..

Finally, set up the virtual environment for the workflow

pyenv virtualenv 3.11 walter
pyenv activate walter
pip install -r requirements.txt

Running walter

Example run

./walter.sh -c /users/user/scratch/config.yml -e slurm

For more details, execute ./walter.sh --help.