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The absolute path to the batch script. This script must contain the batch job submission command (bsub for LSF / sbatch for SLURM). It gives the user the ability to customize the the batch submission. Overall, it can act as a wrapper for the code that will do the analysis on the data along with submitting the job.

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The parameters that will be passed to the executable as command line arguments.  These parameters can be used as parameters to the bsub/sbatch command to specify the queue, number of cores etc. Or; they can be used to customize the script execution. In addition, details of the batch job are made available as as environment variables.

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For example, to update the status of the job using bash, one can use 

curl -s -XPOST ${JID_UPDATE_COUNTERS} -H "Content-Type: application/json" -d '[ {"key": "<b>LoopCount</b>", "value": "'"${i}"'" } ]'

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The logger.debug statements are sent to the job's log file. Note, one can form bsub/ sbatch commands where the log output is not sent to a logfile and is instead sent as an email. Part of an example log file output is shown below.

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