Galaxy Mcp

Overview

Galaxy Mcp is a Model Context Protocol server that connects AI assistants to the Galaxy bioinformatics platform. It lets you execute Galaxy tools and manage workflows directly from Claude, Cursor, VS Code, and other MCP clients, turning your AI assistant into a gateway for genomics and data analysis work.

The server runs locally on your machine via the uvx galaxy-mcp command. You'll need to provide two environment variables: GALAXY_URL and GALAXY_API_KEY to authenticate with your Galaxy instance. Version 1.3.0 is the current release, distributed under the MIT license with source code available at galaxyproject/galaxy-mcp on GitHub.

Galaxy Mcp sits in the Development category on mcp.site and works with MCP clients including Claude Desktop, Claude Code, Cursor, VS Code, Windsurf, and Zed. If you're the maintainer at the Galaxy Project, you're welcome to claim this listing to verify ownership and keep the information accurate.

Installation

// claude_desktop_config.json
{
  "mcpServers": {
    "galaxy_mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<galaxy-url>",
        "GALAXY_API_KEY": "<galaxy-api-key>"
      }
    }
  }
}

Requires GALAXY_URL, GALAXY_API_KEY