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CWL runner for Kubernetes

Project description

calrissian

CWL on Kubernetes

CircleCI

Overview

Calrissian is a CWL implementation designed to run individual steps as Pods in a kubernetes cluster

It is in development and includes a simple workflow (revsort single / array) to reverse and sort the contents of text files.

Preparing Openshift

The openshift/ directory contains YAML files that demonstrate the basic functionality. To configure Openshift, do the following:

  1. Create a project in openshift (e.g. calrissian). Note that namespaces must be unique, so if calrissian is already in use on the cluster, you will need to choose a different name here and other places where the namespace is referenced.

     oc new-project calrissian
    
  2. Create a role in your project to allow managing Pods:

     oc create role pod-manager-role --verb=create,delete,list,watch --resource=pods
    
  3. Bind your project's default service account access to these roles. Calrissian running inside the cluster will use this service account to make Kubernetes API calls.

     oc create rolebinding pod-manager-default-binding --role=pod-manager-role --serviceaccount=calrissian:default
    
  4. Create the BuildConfig - this allows Openshift to build the source code into a Docker image and starts a build automatically. If you wish to build a different branch or repo, edit this file.

     oc create -f openshift/BuildConfig.yaml
    
  5. Create the VolumeClaims - these are the storage locations that will be shared between pods, and must support read-write many access.

     oc create -f openshift/VolumeClaims.yaml
    

Running the example

With the VolumeClaims and Build processes in place, you can run the example with 2 jobs. These jobs use the docker image built by the BuildConfig, so they cannot be run until the build completes.

  1. Stage the input data and workflow onto the input-data volume with the StageInputDataJob.

     oc create -f openshift/StageInputDataJob.yaml
    
  2. Run the workflow engine with the CalrissianJob

     oc create -f openshift/CalrissianJob-revsort.yaml
    
  3. Job pods can be monitored from the openshift web interface or via command-line

     oc logs -f job/calrissian-revsort-array
    

Notes

  1. Calrissian will delete completed jobs for individual steps, but you may want to delete the calrissian-revsort-array job manually after running it.

Project details


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Files for calrissian, version 0.2.0
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