zoo-calrissian-runner

Python library for bridging ZOO-Project execution context and Calrissian

🔗 Dependencies

This runner now uses zoo-runner-common and zoo-template-common for shared functionality, eliminating duplicated code.

Key changes:

• ✅ Inherits from BaseRunner for common methods
• ✅ Uses shared ZooConf, ZooInputs, ZooOutputs, CWLWorkflow classes
• ✅ ExecutionHandler inherits from CommonExecutionHandler (from zoo-template-common)
• ✅ Focuses only on Calrissian/Kubernetes-specific logic

Installation

Install with zoo-runner-common dependency:

pip install zoo-calrissian-runner
# Or from source:
pip install -e . 

Environment variables

• STORAGE_CLASS: RWX storage class (use "hostpath" for Docker Desktop on Mac)
• CALRISSIAN_IMAGE: Calrissian container image
• DEFAULT_VOLUME_SIZE: default size for RWX storage volume
• DEFAULT_MAX_CORES: maximum number of cores if CWL doesn't specify resource requirements
• DEFAULT_MAX_RAM: maximum RAM (in MB) if CWL doesn't specify resource requirements

CWL wrapper templates:

• WRAPPER_STAGE_IN
• WRAPPER_STAGE_OUT
• WRAPPER_STAGE_MAIN
• WRAPPER_STAGE_RULES

Running the tests

Add a tests/.env file including the values with::

CR_USERNAME=""
CR_TOKEN=""
CR_ENDPOINT="https://index.docker.io/v1/"
CR_EMAIL=""
AWS_SERVICE_URL=""
AWS_REGION=""
AWS_ACCESS_KEY_ID=""
AWS_SECRET_ACCESS_KEY=""

KUBECONFIG=""
STORAGE_CLASS=""

DEFAULT_MAX_CORES=8
DEFAULT_MAX_RAM=1024
DEFAULT_VOLUME_SIZE=10000 # mebibytes (2**20)


ADES_STAGEOUT_OUTPUT=""