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Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation
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Based on SOC occupation classification
Use when authoring a Galaxy User-Defined Tool (UDT) -- a `class: GalaxyUserTool` YAML definition that wraps a container and command into a tool a non-admin user creates and runs (e.g. via Galaxy MCP create_user_tool / run_user_tool, or POST /api/unprivileged_tools). Not for classic XML/ToolShed tool wrappers.
Use this skill when asked to create, draft, or write a Galaxy workflow report template for the Workflow Editor's Report tab. Triggers on requests like "create a report for this workflow", "draft a workflow report template", "write a Galaxy report for workflow <id/url>".
Galaxy Collection Transformation Command - transform Galaxy dataset collections reproducibly using Galaxy's native tools. Use when asked to filter, sort, relabel, restructure, flatten, nest, merge, or otherwise manipulate Galaxy collections.
Galaxy MCP server tools reference for histories, datasets, tools, and workflows
Building UCSC Track Hubs (track hubs and assembly hubs) — bigBed/bigChain/bigMaf format requirements, composite-track rules, hub.txt / genomes.txt / trackDb.txt structure. Use when emitting a UCSC hub from Galaxy outputs, wrapping a hub-publishing tool, or debugging hubCheck failures.
Galaxy tool development reference — creating new tools, testing, IUC review preparation, and updating existing tools. Use when authoring or modifying Galaxy tool wrappers for tools-iuc.
| name | galaxy-integration |
| description | Router for Galaxy MCP, JupyterLite notebooks, and BioBlend automation |
| user_invocable | true |
Use Galaxy MCP and BioBlend-based scripts to interact with a Galaxy instance for tool discovery, workflow validation, and workflow testing.
Route to the appropriate sub-skill based on task:
| Task | Sub-Skill | Location |
|---|---|---|
| Write JupyterLite notebook | jupyterlite-galaxy | jupyterlite/SKILL.md |
| MCP tools reference | galaxy-mcp-reference | mcp-reference/SKILL.md |
| History/dataset access | - | mcp-reference/history-access.md |
| Common gotchas | - | mcp-reference/gotchas.md |
| BioBlend batch scripts | - | scripts/galaxy_tool_checker.py |
| Tool checking examples | - | examples/tool-checking.md |
| Workflow testing examples | - | examples/workflow-testing.md |
The base URL of the Galaxy server:
https://usegalaxy.org/https://usegalaxy.eu/http://localhost:8080/In Galaxy UI: User -> Preferences -> Manage API Key
.env (recommended)cp .env.example .env
nano .env
Set:
GALAXY_URL=https://usegalaxy.org/
GALAXY_API_KEY=your_actual_api_key_here
Galaxy MCP when:
BioBlend script (scripts/galaxy_tool_checker.py) when:
Confirm MCP connectivity
README.md for configurationTool discovery
search_tools_by_name(query=...)
get_tool_details(tool_id=..., io_details=True)
Workflow testing loop
create_history(history_name=...)
invoke_workflow(workflow_id=..., inputs=..., history_id=...)
get_history_contents(history_id=...)
# Fix and repeat
When reporting MCP results:
README.mdgalaxy-integration.md