Galaxy MCP Server

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.

Project Overview

The repository holds two independent implementations of the same Galaxy operation set, and the contract that keeps them in step:

• python/ -- the Python MCP server, published to PyPI as galaxy-mcp. It reaches Galaxy through BioBlend. See the Python README.
• typescript/ -- a pnpm workspace published to npm as @galaxyproject/galaxy-ops, galaxy-cli and galaxy-mcp: one framework-free core (galaxy-ops) with a command line and a stdio MCP server on top. See the TypeScript README.
• contract/ -- what both are held to: the Python surface manifest, golden results replayed through both, the snapshot of Galaxy's built-in server, and the registry of known differences. See the contract README.

The two are meant to stay in step: an operation keeps its name and its meaning across both. They are still separate codebases with separate release trains, though, so each README lists the operations that surface actually has -- read the one you are using.

ROADMAP.md explains why there are two implementations, how they relate to Galaxy's built-in MCP server, and what comes next. PARITY.md is the generated, CI-checked record of where they differ.

Key Features

• 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 the tool catalog, inspect a tool's inputs, and execute Galaxy tools
• User-Defined Tools: Create, list, run, and deactivate unprivileged user-defined tools
• Workflow Integration: Find and import workflows from the Intergalactic Workflow Commission (IWC), then invoke them and follow their invocations
• History Operations: Manage Galaxy histories, datasets, and collections, and inspect the jobs behind them
• File Management: Upload files to Galaxy from local storage or from a URL, and download results back
• Pages: Read and write Galaxy-flavored markdown pages -- history-attached notebooks and standalone reports -- including their revision history
• Verified Container Recommendation (optional): Resolve a real quay.io/biocontainers image for a set of conda packages instead of guessing one -- see Optional extras
• Mock-based test suite: The default suite runs entirely against mocked Galaxy responses, so it needs no server; a separate suite against a live Galaxy is opt-in and skips when no credentials are configured

Optional extras

container-recommend

Enables the recommend_biocontainer tool, which resolves a verified quay.io/biocontainers image for a set of conda packages. Authoring a user-defined tool means naming a container, and a hallucinated image tag is the most common way a UDT passes validation and then dies at run time with manifest unknown. This wraps galaxy.tool_util.deps.mulled.recommend -- the same resolver Galaxy's own custom-tool agent uses (added in Galaxy 26.1, galaxyproject/galaxy#22981) -- so the image is checked against quay.io rather than invented.

It is an extra rather than a hard dependency because galaxy-tool-util pulls in lxml and conda-package-streaming, and every other tool on this server works without it. The tool is only registered when the extra is installed, so a stock install simply doesn't advertise it.

uvx --from 'galaxy-mcp[container-recommend]' galaxy-mcp
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... [View full README on GitHub](https://github.com/galaxyproject/galaxy-mcp#readme)