slurm
This profile configures Snakemake to run on the SLURM Workload Manager
Setup
Deploy profile
To deploy this profile, change to your desired working directory and run
cookiecutter https://github.com/Snakemake-Profiles/slurm.git
Then, you can run Snakemake with
snakemake --profile slurm ...
Resources
The following resources are supported by on a per-rule bassis:
mem - set the memory resource request in mb. walltime, runtime - set the time resource in min.
Tests
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