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#ISB-CGC Compute Examples

This repo contains computational examples for use in conjunction with the ISB-CGC platform.

Current examples include how to run CWL workflows on a single VM, and how to use Grid Engine. Additional examples will be added as new use-cases are defined and implemented.

  • Running CWL workflows on the google cloud using the cwl_runner script.

    • modification of the (now unsupported) google script to allow automated workflow runs in the cloud
  • Using CWL (Common Workflow Language)

    • cwl-examples: Several examples of specific CWL workflows.
  • Using Grid Engine

    • grid-engine: An example using Elasticluster to create clusters of GCE VMs running Grid Engine. (This example was inspired by the Google Genomics example described here. Please be sure to also have a look at their other data-processing examples!)