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Snakemake-Profiles / lsf

Snakemake profile for running jobs on an LSF cluster
MIT License
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update jobid/log splitting for snakemake v7.1.1 #46

Closed ASLeonard closed 2 years ago

ASLeonard commented 2 years ago

The changes for multicluster support in snakemake v7.1.1 break the current lsf profile, so this resolves that behaviour. Probably a nicer way to split the args, but just a quick fix.

mbhall88 commented 2 years ago

Thanks @ASLeonard. Are you able to provide an example of what arguments are being passed to the profile before and after the update?

ASLeonard commented 2 years ago

Not sure if this is what you meant, but the error looked like

  File ".../lsf_status.py", line 199, in <module>
    jobid = int(sys.argv[1])
ValueError: invalid literal for int() with base 10: '208120342 logs/<rule>/<wildcards>.out'

Since the multicluster update in v7.1.1 now quotes both the jobid and the log name (passing "<jobid> <log>"), so sys.argv[1] now captures both. Before it probably would be <jobid> <log> before, correctly filling sys.argv[1] and sys.argv[2].

mbhall88 commented 2 years ago

Closing in favour of #47

ASLeonard commented 2 years ago

Thanks, totally forgot about pre-change behaviour, so nice fix!