NCBI-Hackathons/NovoGraph

bsub for CALLMAFFT.pl

christinawu2008 opened this issue · 1 comments

christinawu2008 commented

Hi Evan,

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

Thanks

Cheers,
Chen

evanbiederstedt commented

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: #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