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dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.
MIT License
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Converting from SLURM to SGE #90

Closed TamaraO closed 6 years ago

TamaraO commented 6 years ago

Can the script be adapted to run multiple samples in parallel on SGE (versus SLURM)? Despite my best efforts to parallelize samples on SGE, they always run sequentially. Thank you!

eboileau commented 6 years ago

I am not familiar with SGE, however this should be possible. For e.g. when calling run_all_rpbp_instances with --use-slurm, each sample in the loop is submitted via sbatch using the call job_id = slurm.check_sbatch(cmd, args=args) (line 181). This function wraps calls to sbatch, so for SGE I guess you'd have to wrap calls to qsub. You can have a look in the requirement package misc.slurm (pymisc-utils/misc/slurm.py). Let me know how it goes.