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opencb / opencga

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is maintained and develop by its parent company Zetta Genomics. Please contact support@zettagenomics.com for bug report and feature requests.
Apache License 2.0
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How to use SGE with OpenCGA #1659

Open Mohammedhusen opened 4 years ago

Mohammedhusen commented 4 years ago

Hi Team,

We have SGE scheduler and need your help to configure with OpenCGA, could you please share if you have any documents or step to configure SGE.

Thanks for your all support.

Mohammedhusen commented 4 years ago

Hi Team,

Could you please update on this?

j-coll commented 3 years ago

Hi @Mohammedhusen ,

To use SGE you should first configure the "analysis.execution" section in the configuration.yml file with the default queue that you want to use

analysis:
  execution:
    # Accepted values are "local", "SGE", "azure-batch", "k8s"
    # see org.opencb.opencga.master.monitor.executors.ExecutorFactory
    id: "SGE"
    defaultQueue: "???"            # Default queue to be used to submit jobs

The OpenCGA Master (opencga-admin.sh catalog daemon --start ) should be running in a node with access to the SGE commands, i.e. "qsub", "qacct" and "qstat"

Also, I should warn that this executor is not being actively maintained, so it might throw some errors. If that's the case, please let me know and I'll try to fix them.

j-coll commented 3 years ago

In case that you are using OpenCGA v1.4.x, the configuration.yml section to modify is this one:

execution:
  mode: "SGE"
  defaultQueue: "???"