LSF cluster usage - Githubissues

GooglingTheCancerGenome / sv-callers

Snakemake-based workflow for detecting structural variants in genomic data

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Closed TnakaNY closed 1 year ago

TnakaNY commented 4 years ago

HI, Could you provide example command to submit a job to LSF cluster? I am not a specialist for job scheduler.

Thanks.

arnikz commented 4 years ago

Hi,

Sorry, I don't have access to test on a LSF cluster. Use the bsub command directly rather than xenon (LSF is not supported yet).

Something like:

SUBMIT_CMD="bsub \
-J smk.{rule} \
-cwd \
-T {threads} \
-W 15 \
-M {resources.mem_mb} \
-o stdout-%J.log \
-e stderr-%J.log"

snakemake --use-conda --cluster "${SUBMIT_CMD}"... (see README and this blog).

Cheers, Arnold

TnakaNY commented 4 years ago

I see. Thank you for quick reply!

jmaassen commented 4 years ago

We could add LSF to xenon provided we find a way to properly test it (preferably using an LSF docker image).

xiaojingshi commented 3 years ago

I see. Thank you for quick reply!

Hi, will you be able to share your command to submit a job to LSF cluster? Thank you very much.