diff --git a/README.md b/README.md index defb93da3bff6d2b046ec9c9e5fa71e614627e05..ba313e8492aba703a77224260b595135ab028c24 100644 --- a/README.md +++ b/README.md @@ -86,10 +86,18 @@ Execute the workflow locally via `snakemake --use-singularity --singularity-args "-B '/home/login/'" --cores $N` -using $N cores or run it in a cluster environment via +using $N cores or run it in a cluster environment via this standard command line : `snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1` +Or specifically on Slurm cluster: + +`sbatch snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores $SLURM_JOB_CPUS_PER_NODE` + +or on SGE cluster: + +`snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "qsub -cwd -V -b y -l h_vmem={cluster.ram} -pe [PE] {threads}" -j 200 --nolock --cores 1` + Visualize how the rules are connected via