hpc-configurations

HPC Cluster Schedulers

HPC Systems using Singularity will require a cromwell configuration file to be included for every execution.

#config='lsf.conf' or 'slurm.conf'
java -Dconfig.file=$config -jar cromwell.jar run seaseq-case.wdl -i inputs.json -o options.json

The configuration file contains the needed commands to submit and monitor singularity executions.

We provided configuration files for the different schedulers:

1. IBM SPECTRUM LSF requires the lsf.conf file, and a check-job-alive script to be included in your $PATH

   # Run the following commands to put it in your $PATH:
   wget https://raw.githubusercontent.com/stjude/seaseq/master/docs/hpc-configurations/check-job-alive
   mv check-job-alive ~/bin/

2. SLURM only requires the slurm.conf file.