scripts/BatchJobs/README.md

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

batchtools should be preferred over BatchJobs. See scripts in scripts/batchtools.

Running PopSV in a HPC using BatchJobs

Place in the working directory:

• automatedPipeline-BatchJobs.R which contains the pipeline functions.
• BatchJobs_profile.R, the configuration file for BatchJobs.
• abacus.tmpl, a template for a job in your HPC (here Abacus at McGill's Genome Center).
• makeClusterFunctionsAdaptive, the function to read the template file.

Then in a R script, call the functions like in run-PopSV-batchjobs-automatedPipeline.R (or copy and edit this script).

Configuring your HPC

We used BatchJobs on TORQUE HPC only. Other HPC systems could be configured (see BatchJobs doc) but we recommend using batchtools instead with the configuration in scripts/batchjobs.

TORQUE is used at McGill's Genome Center on Abacus and by Compute Canada on Guillimin.

To configure BatchJobs from these files, you should:

1. Check the name of the template file called in BatchJobs_profile.R. Currently guillimin.tmpl. Change to abacus.tmpl for Abacus.
2. Check the commands in makeClusterFunctionsAdaptive.R. Currently qsub/canceljob/qstat. Some HPC prefer msub, showq, qdel, etc.

When running the pipeline on Guillimin, add other.resources=list(supervisor.group="XXXXX") with the account to use. This should be added as an argument of the autoGCcounts, autoExtra and autoNormTest functions.

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.