This profile configures Snakemake to run on the SLURM Workload Manager
To deploy this profile, run
mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
cookiecutter https://github.com/Snakemake-Profiles/slurm.git
Then, you can run Snakemake with
snakemake --profile slurm ...
The following resources are supported by on a per-rule basis:
- mem: set the memory resource request in mb.
- walltime, runtime: set the time resource in min.
Test-driven development is enabled through the tests folder. Provided that the user has installed docker and enabled docker swarm, the SLURM tests will download two images:
In addition, testing of the cookiecutter template itself is enabled through the pytest plugin for Cookiecutters. You can run the tests by issuing
pytest -v -s