Configure GotCloud

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Configure GotCloud

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The GotCloud software relies on configuration files to make it as flexible as possible. You will not need to set or know about most of the settings, however, there are some things you'll want to know about to make using GotCloud as simple to use as possible.

Configure Your Batch Environment

GotCloud supports two options to allow you to submit the work from the aligner and umake to run on your local cluster. There are many different types of clusters and the details of their interfaces vary for each installation. As distributed GotCloud contacts support for these:

  • MOSIX
  • SGE (Sun Grid Engine)
    • Used by StarCluster
  • SLURM
  • PBS (Portable Batch System)

You can specify the type of cluster with the option -batchtype. In addition you can pass options to that cluster system with the option -batchopt.

  • Alternatively, you can set them using BATCH_TYPE and BATCH_OPTS in the configuration file.

For example, here are examples of invocations of the aligner using these batch systems:

gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"

gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"
gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"

gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype sge

The interface to actually submit a job to a cluster is coded in scripts/runcluster.pl (probably installed in /usr/local/gotcloud). You may need to (and should) modify this code to work with your particular cluster system, whether it be to handle options in some manner or add an entirely new batchtype.