Starting snakemake in SLURM - JoshLoecker/MAPT GitHub Wiki

View the Simple SLURM Job for definitions on #SBATCH

In this job we are going to be running a snakemake dry-run within SLURM. In this script, we are doing the following

  1. Sourcing our .bashrc
  2. Activating the mapt_pipeline conda environment
  3. Change directories to the pipeline directory
  4. Execute a snakemake dry run
#!/bin/bash
#SBATCH --job-name="snakemake"
#SBATCH -p debug
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 00:00:30
#SBATCH -o "snakemake_output"
#SBATCH -e "snakemake_output"

source ~/.bashrc
conda activate /project/brookings_minion/conda-envs/mapt_pipeline
cd /project/brookings_minion/examples/MAPT
snakemake -j all --use-singularity -n