syqada batchΒΆ

syqada batch requires two arguments, a batch directory and –step, which has three options.

  • init
  • repend
  • rerun
  • run

init and repend|rerun are mutually exclusive. run can be invoked alone or with one of the others.

Most typical usages of syqada batch have been replaced by running syqada auto and letting it figure out what to do. There are two special cases described here.

When a failure has occurred, and you wish to reset the batch to re-run.:

>>> syqada batch *batchroot* --step repend [run]

This cleans up the logs of the failed jobs in the given task directory and restores the failed scripts to the PENDING directory so the batch can be resumed. Run is optional, because you might choose to use syqadaf auto after re-pending the failed jobs. Examples can be found in Troubleshooting Guide or the Preface to the Tutorials.

The second usage is to run a batch whose memory and processor configuration would run more jobs at once than you wish to, if, say, you are trying to share the machine with a team member working a project with a shorter deadline, or if you have a batch whose success depends on serial execution of the jobs (variant_tools sample import, for instance, seems safest run in serial mode).

>>> syqada batch *batchroot* --max_bolus N

will constrain SyQADA to submit no more than N jobs at once.

>>> syqada batch *batchroot* --prototype
When running syqada auto or batch, –prototype creates all the jobscripts for the desired step and then runs only one of them, quitting without submitting the remainder if that job fails. If the job succeeds, syqada proceeds as usual and a normal bolus of the remaining jobs is submitted for execution.