galaxy-automation - Automate Galaxy workflows with BioBlend and Planemo
Automates Galaxy workflows through BioBlend and Planemo, including invocation, status monitoring, error handling, batch processing, and dataset management.
Tags
Updated: 2026-10-08Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Connect to Galaxy servers
- Manage Galaxy histories
- Invoke Galaxy workflows
- Poll invocation statuses
- Handle workflow failures
- Rerun failed invocations
- Upload and inspect datasets
- Create dataset collections
- Test workflows with Planemo
- Process batches programmatically
Inputs
- Galaxy server URL
- Galaxy API key
- Workflow ID
- History ID or name
- Workflow input mappings
- Dataset files or IDs
- Dataset collection IDs
- Rerun parameters
- Job YAML file
- Polling settings
Outputs
- Invocation IDs
- Invocation status updates
- Workflow step statuses
- Failure classifications
- Uploaded datasets
- Dataset collections
- History contents
- Workflow test results
- Error messages
Requirements
- Python runtime
- BioBlend package
- Planemo package
- Galaxy server access
- Valid Galaxy API key