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NCBI-Hackathons / NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies
MIT License
44 stars 8 forks source link

bsub for CALLMAFFT.pl #15

Open christinawu2008 opened 5 years ago

christinawu2008 commented 5 years ago

Hi Evan,

Simply changing --qsub to --bsub won't help... can we have a script for bsub batch system?

Thanks

Cheers, Chen

evanbiederstedt commented 5 years ago

Hi @christinawu2008

Sorry I just saw this; I've been occupied with other things.

Yes! It should be possible to add LSF compatibility to this script. @nhansen did something similar here with TORQUE. See here: https://github.com/NCBI-Hackathons/NovoGraph/pull/19

The documentation for LSF job arrays is detailed here:, which explains the syntax needed https://www.ibm.com/support/knowledgecenter/en/SSWRJV_10.1.0/lsf_admin/job_arrays_lsf.html

The problem I see is that given how LSF is set up, this will be system-specific. For instance, you could either configure LSF to allocate resources by job or by core.

If you could test out the syntax which works for you locally, we'd be happy to add in this feature. Please let us know if you follow the logic of the perl script, and we could explain further.

Thanks, Evan