@galaxyproject/galaxy-mcp

A Model Context Protocol server (Node) that exposes Galaxy agent operations -- histories, datasets, tools, workflows, and the IWC catalog -- as MCP tools over stdio. Built on @galaxyproject/galaxy-ops.

Install / run

GALAXY_URL=https://usegalaxy.org/ GALAXY_API_KEY=your-api-key \
  npx @galaxyproject/galaxy-mcp
# -> "galaxy-mcp: connected on stdio"

Requires Node.js >=22.19. The server reads GALAXY_URL and GALAXY_API_KEY from the environment and speaks MCP over stdio.

Use with an MCP client

For example, in Claude Desktop's claude_desktop_config.json:

{
  "mcpServers": {
    "galaxy": {
      "command": "npx",
      "args": ["-y", "@galaxyproject/galaxy-mcp"],
      "env": {
        "GALAXY_URL": "https://usegalaxy.org/",
        "GALAXY_API_KEY": "your-api-key"
      }
    }
  }
}

Every operation is registered as an MCP tool; read-only operations are flagged with readOnlyHint.

Documentation

See the galaxy-agent-tools workspace README for the full list of operations exposed as tools.

License

MIT