https://github.com/gagneurlab/snakemake-slurm-template

https://github.com/gagneurlab/snakemake-slurm-template

Last synced: 2 months ago
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• Host: GitHub
• URL: https://github.com/gagneurlab/snakemake-slurm-template
• Owner: gagneurlab
• License: mit
• Created: 2023-03-15T21:24:33.000Z (about 2 years ago)
• Default Branch: master
• Last Pushed: 2023-05-11T11:37:16.000Z (about 2 years ago)
• Last Synced: 2025-01-25T04:29:22.931Z (4 months ago)
• Language: Python
• Size: 37.1 KB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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 ` call with `run_slurm_jobs `

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`