Automating Galaxy Workflows

The BioBlend library can be used to invoke and monitor Galaxy workflows. Planemo provides a higher-level interfaces to working with workflows - both as a Python library and via the command line. Planemo can take care of orchestrating details such as launching and configuring a Galaxy instance, installing required tools for the workflow, monitoring the workflow invocation, and downloading the results back to a local directory.

planemo run workflow.ga job.yml

The format of the job file should be YAML or JSON and matches the job definition used by the workflow test format.

A job template for a particular workflow can be created with the workflow_job_init command.

planemo workflow_job_init my-workflow.ga

This will create a my-workflow-job.yml file in the current directory.

Planemo run and the underlying Python code when used as a library support a wide range of arguments for how to run a Galaxy workflow.