CWL runner for Kubernetes
CWL on Kubernetes
Calrissian is a CWL implementation designed to run individual steps as Pods in a kubernetes cluster
openshift/ directory contains YAML files that demonstrate the basic functionality. To configure Openshift, do the following:
Create a project in openshift (e.g.
calrissian). Note that namespaces must be unique, so if
calrissianis 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
Create a role in your project to allow managing
oc create role pod-manager-role --verb=create,delete,list,watch --resource=pods
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
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
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.
Stage the input data and workflow onto the
input-datavolume with the StageInputDataJob.
oc create -f openshift/StageInputDataJob.yaml
Run the workflow engine with the CalrissianJob
oc create -f openshift/CalrissianJob-revsort.yaml
Job pods can be monitored from the openshift web interface or via command-line
oc logs -f job/calrissian-revsort-array
- Calrissian will delete completed jobs for individual steps, but you may want to delete the
calrissian-revsort-arrayjob manually after running it.
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