Galaxy MCP Server

MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows. That is what the galaxy mcp server brings to an AI assistant: the same capability, reachable through the Model Context Protocol rather than a separate app or dashboard.

The short version

This project provides a Model Context Protocol (MCP) server for interacting with the Galaxy bioinformatics platform. It enables AI assistants and other clients to connect to Galaxy instances, search and execute tools, manage workflows, and access other features of the Galaxy ecosystem.

• Galaxy Connection — Connect to any Galaxy instance with a URL and API key
• OAuth Login (optional) — Offer browser-based sign-in that exchanges credentials for temporary Galaxy API keys
• Server Information — Retrieve comprehensive server details including version, configuration, and capabilities
• Tools Management — Search, view details, and execute Galaxy tools
• Workflow Integration — Access and import workflows from the Interactive Workflow Composer (IWC)
• History Operations — Manage Galaxy histories and datasets

Getting it running

Because this one is hosted, setup is mostly authentication — you point your client at the endpoint and approve access. Nothing runs on your machine, so there is no runtime to keep patched.

What it needs from you

Configuration is passed through the environment: GALAXY_URL, GALAXY_API_KEY, GALAXY_MCP_PUBLIC_URL, GALAXY_MCP_SESSION_SECRET, GALAXY_SERVER. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.

Things to watch

• Your data travels to the provider's service, so the usual questions apply about what you send and what they retain.
• Missing credentials fail quietly in some clients — if no tools show up, check the environment block first.
• Keep per-call confirmation enabled while you learn its behaviour; it is the cheapest safeguard you have.

How it compares

This sits in the browser automation group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. It is maintained by galaxyproject; worth a glance at recent repository activity before you build anything load-bearing on it.

We check each listing at SyncDev against the project's documentation before it goes live — if something here drifts out of date, it is a bug worth reporting.