Galaxy MCP Server

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

This repository contains a Python-based MCP server implementation that provides comprehensive integration with Galaxy's API through BioBlend.

In addition to the Python server, this repository now includes a TypeScript workspace in galaxy-agent-tools/ that offers the same Galaxy operations two ways: a galaxy-cli command-line tool and a galaxy-mcp (Node) MCP server, built on a shared core and kept in lockstep with this server's toolset. See the galaxy-agent-tools README to build and use it.

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, 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
• File Management: Upload files to Galaxy from local storage
• Comprehensive Testing: Full test suite with mock-based testing for reliability

Quick Start

The galaxy-mcp CLI ships with both stdio (local) and HTTP transports. Choose the setup that matches your client:

# Stdio transport (default) – great for local development tools
uvx galaxy-mcp

# HTTP transport with OAuth (for remote/browser clients)
export GALAXY_URL="https://usegalaxy.org.au/"          # Target Galaxy instance
export GALAXY_MCP_PUBLIC_URL="https://mcp.example.com" # Public base URL for OAuth redirects
export GALAXY_MCP_SESSION_SECRET="$(openssl rand -hex 32)"
uvx galaxy-mcp --transport streamable-http --host 0.0.0.0 --port 8000

When running over stdio you can provide long-lived credentials via environment variables:

export GALAXY_URL="https://usegalaxy.org/"
export GALAXY_API_KEY="your-api-key"

For OAuth flows the server exchanges user credentials for short-lived Galaxy API keys on demand, so you typically leave GALAXY_API_KEY unset.

For non-OAuth HTTP clients, connect(url=..., api_key=...) stores Galaxy credentials per MCP session rather than globally. Clients normally preserve MCP sessions by default, which allows multiple users to share the same MCP server while keeping their Galaxy credentials isolated.

Alternative Installation

# Install from PyPI
pip install galaxy-mcp

# Run (stdio by default)
galaxy-mcp

# Or from source using uv
cd mcp-server-galaxy-py
uv sync
uv run galaxy-mcp --transport streamable-http --host 0.0.0.0 --port 8000

Container Usage

The published image defaults to stdio transport (no HTTP listener):

docker run --rm -it \
  -e GALAXY_URL="https://usegalaxy.org/" \
  -e GALAXY_API_KEY="your-api-key" \
  galaxyproject/galaxy-mcp

For OAuth + HTTP:

docker run --rm -it -p 8000:8000 \
  -e GALAXY_URL="https://usegalaxy.org.au/" \
  -e GALAXY_MCP_TRANSPORT="streamable-http" \
  -e GALAXY_MCP_PUBLIC_URL="https://mcp.example.com" \
  -e GALAXY_MCP_SESSION_SECRET="$(openssl rand -hex 32)" \
  galaxyproject/galaxy-mcp

Connect to Claude Desktop

• Ensure that GalaxyMCP runs with uvx galaxy-mcp
• Add export GALAXY_SERVER=https://usegalaxy.org to your .bashrc (or equiv)
• Download and install claude desktop
• Go to Settings -> Developer -> Edit Config
• Add this to claude_desktop_config.json

{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": ["galaxy-mcp"],
      "env": {
        "GALAXY_URL": "https://usegalaxy.org",
        "GALAXY_API_KEY": "SECRETS"
      }
    }
  }
}

• Under the developer menu, you should now see galaxy-mcp as running (you may need to restart Claude desktop)
• Prompt Claude with "can you connect to galaxy"
• If you have not provided the optional env config you'll be asked for connection details which you can provide like "Use my Galaxy API key: XXXXXXX"
• Talk to Claude to work with your galaxy instance, e.g. "give a summary with my histories"

Development Guidelines

See the Python implementation README for specific instructions and documentation.

License

MIT