io.github.galaxyproject/galaxy-mcp

io.github.galaxyproject/galaxy-mcp

MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows

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Connect this server

Add this to your MCP client config — claude_desktop_config.json (Claude Desktop) or .cursor/mcp.json (Cursor).Suits: Claude Desktop · Cursor.

{
  "mcpServers": {
    "galaxy-mcp": {
      "command": "uvx",
      "args": [
        "galaxy-mcp"
      ],
      "env": {
        "GALAXY_URL": "<your GALAXY_URL>",
        "GALAXY_API_KEY": "<your GALAXY_API_KEY>"
      }
    }
  }
}
Environment variables
  • GALAXY_URLrequiredURL of the Galaxy instance to connect to (e.g., https://usegalaxy.org)
  • GALAXY_API_KEYrequiredsecretAPI key for authenticating with the Galaxy instance

A starting point — check the repository for exact arguments and setup. Restart your client after editing the config.

Category
Developer Tools
Version
1.3.0
Registry
active
Published
1/29/2026

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