A useful function of the LSF cluster management system is the use of job arrays. They enable you to submit many jobs at the same time that differ by only one parameter, such as input file or something. In this case all the jobs are actually identical as they are randomly permuting an input file and scoring the results. So I am using this as a way of making more iterations of the job run in the same time.
bsub -q qname -J "jobName[1-1000]%240" -o /dev/null '~/script/script_name.pl inputFile $(echo $LSB_JOBINDEX).txt option1 option2'
You could also use them to run the same script on many input files, or run with a range of parameters too. I have another use of them where I compare many position weight matrices to a sequence using a job array, one job for each PWM.
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