This profile configures Snakemake to run on Compute Canada with SLURM (e.g. graham).
Note: the default options already use the --use-singularity and --use-envmodules flags, and the ctb-akhanf compute allocation account.
Install cookiecutter on your system (make sure you have python3 loaded):
pip install cookiecutter --user
To deploy this profile, run the following on the login node (e.g. graham):
cookiecutter gh:khanlab/cc-slurm -o ~/.config/snakemake -f --no-input
If you are not using the ctb-akhanf account, or want to customize the options, use this instead:
cookiecutter gh:khanlab/cc-slurm -o ~/.config/snakemake -f
Then, you can run Snakemake with:
snakemake --profile cc-slurm ...
The following resources are supported by on a per-rule basis:
mem_mb - set the memory resource request (megabytes).
time - set the walltime resource (minutes).
gpus - set the number of gpus (defaults to 0).