LSF Example

Here is an example of a submission for a LSF cluster. Of course, you may have to update it based on how your cluster has been set up.

nohup \
snakemake \
--snakefile $SCEQTL_PIPELINE_SNAKEFILE \
--configfile $SCEQTL_PIPELINE_CONFIG \
--rerun-incomplete \
--jobs 20 \
--use-singularity \
--restart-times 2 \
--keep-going \
--cluster \
  "bsub \
  -W 24:00 \
  -x \
  -M 10000 \
  -e $LOG \
  -o $LOG" \
> $LOG/nohup_`date +%Y-%m-%d.%H:%M:%S`.log &