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galaxy-mcp-reference

Document Galaxy MCP server functions for histories, datasets, tools, and workflows.

7|12|Updated Dec 17, 2025
Search Tags:#automation#API#reference#workflows#datasets#histories#galaxy-mcp
One-click install
npx skills add https://github.com/galaxyproject/galaxy-skills --skill galaxy-mcp-reference
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: galaxy-mcp-reference
Source: https://github.com/galaxyproject/galaxy-skills/tree/main/galaxy-integration/mcp-reference
Command: npx skills add https://github.com/galaxyproject/galaxy-skills --skill galaxy-mcp-reference

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill provides a complete reference for Galaxy MCP server functions across histories, datasets, tools, workflows, and IWC.

Core Features & Use Cases

  • Comprehensive API reference for MCP server components: histories, datasets, tools, workflows, and IWC.
  • Usage guidance with example MCP calls and common patterns to accelerate integration and automation.
  • Use Case: A developer building Galaxy MCP integrations can quickly locate available endpoints and inspect responses to implement automated workflows.

Quick Start

List histories with their IDs and names to verify connectivity.

Frequently Asked Questions about galaxy-mcp-reference

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I list Galaxy histories using the MCP server?▼

To list Galaxy histories using the MCP server, you reference the mcp__galaxy__list_history_ids function. This call returns available history IDs and names, allowing developers to verify connectivity before retrieving datasets or invoking workflows.

What is the Galaxy MCP server used for?▼

The Galaxy MCP server is used for automating workflows, datasets, and histories in Galaxy deployments. It provides a comprehensive API reference for developers to discover endpoints, examine results, and script MCP-based automations.

Can I invoke Galaxy workflows through the MCP API?▼

Yes, you can invoke Galaxy workflows through the MCP API by using the mcp__galaxy__invoke_workflow call. This function allows developers to programmatically trigger and automate workflow execution within their Galaxy deployments.

How do I retrieve dataset contents from a Galaxy history via MCP?▼

You retrieve dataset contents from a Galaxy history via MCP by using the mcp__galaxy__get_history_contents call. This endpoint allows developers to inspect specific datasets within a history for integration and automation scripting.

Does the Galaxy MCP server support IWC workflows?▼

Yes, the Galaxy MCP server supports IWC workflows as part of its comprehensive API reference. Developers can discover endpoints and examine results specifically for IWC components alongside histories, datasets, tools, and standard workflows.

What do I need to connect to a Galaxy MCP server deployment?▼

To connect to a Galaxy MCP server deployment, you use the mcp__galaxy__connect call. This establishes the initial connection required before you can list histories, retrieve datasets, or invoke workflows for your automation scripts.

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