Utility for running snakemake on SLURM

Features

• Keeps track of running SLURM jobs
• Ends SLURM jobs when cancelling the script
• Saving job logs in logs/ subdirectory
• Allows specifying threads, mem_mb and gpu resources

Usage

1. Copy run_slurm_jobs, slurm_status.py, slurm-status.sh and slurm-sidecar.py into any directory in your $PATH. Make sure that all files are in the same directory.
2. Simply replace your snakemake <additional args> call with run_slurm_jobs <additional args>

Examples:

• run_slurm_jobs.sh --rerun-incomplete --restart-times 3 -k
• It is possible to change slurm arguments and number of total cores on the command line: SNAKEFILE="scripts/Snakefile" N_CORES=256 SBATCH_ARGS="--partition=urgent --exclude=ouga04" run_slurm_jobs.sh --rerun-incomplete -k