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Commit efed741d authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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add cluster command lines

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......@@ -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
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