Auto-generate sge submission scripts - Githubissues

CarragherLab / cptools2

Running cellprofiler on eddie3 / SGE clusters

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Auto-generate sge submission scripts #9

Closed Swarchal closed 6 years ago

Swarchal commented 6 years ago

Made scissorhands to generate qsub scripts.

Now need to:

[x] add scissorhands as a requirement in cptools2
[x] detect number of commands in staging, analysis and destaging jobs
[x] location to save the submission scripts
[x] script name should include datetime to make repeat runs easier
[x] detect user to insert correct path to cellprofiler virtual environment Bonus:
[ ] auto-submit the scripts, though need to run on the staging nodes, don't know how to submit from there