Use Cases

This is a short note on use cases we want to support in the MOLGENIS processing extension

• Share my pipeline
• Add new module
• List my data items
• Incorporate Galaxy or GenePattern? modules in my pipeline
• How did I produce this result file?
• Autogenerate a R-suave (?) document that is executable documentation?
• Export R data annotation packages?

PBS best practices

Overview:

• We use Freemarker to define templates of jobs
• We generate for each job one <job>.sh
• We generate one submit.sh for the whole workflow
• The whole workflow behaves like 'make': it can recover from failure where it left of
• The workflow shares one working directory with conventions to ease inter-step variable passing

Main ingredients:

• The workflow works on a data blackboard
  • The whole workflow uses the same working directory (= blackboard architecture pattern)
  • We use standard file names to reduce inter-step parameter passing (= convention over configuration)
  • Naming convention: <unit of analysis>_<name of step>.<ext>
  • For example in NGS lane (unit) alignment (step): <flowcell_lane>_<pairedalign>.bam
• Make style submit.sh
  • Each line puts one command in the qsub queue
  • We solve dependency ordering using -W depend=afterok:job1:job2 option
  • Use of proper return values will ensure dependent jobs are canceled on fail
• Recoverable steps job<step>.sh
  • We generate a .sh file for each job including standard logging
  • Each script checks if the output is already there (otherwise it can be skipped)
  • Each script checks if it has produced its output (otherwise return error)
  • N.B. check file existence using if ! test -h FILE return -1