This project provides a Model Context Protocol (MCP) server for interacting with the Galaxy bioinformatics platform, enabling AI assistants and other clients to connect to Galaxy instances, search and execute tools, manage workflows, and access other features of the Galaxy ecosystem.
From the registry: MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows
Please install the `galaxy-mcp` MCP server into my current AI client (that's you).
Required prerequisites (do these first if not already done):
- **Galaxy API key** — Get an API key from your Galaxy instance (e.g., usegalaxy.org). For OAuth flows you can leave this unset. (https://usegalaxy.org)
Canonical MCP server config (stdio transport):
- command: `uvx`
- args: ["galaxy-mcp"]
- required environment variables:
- `GALAXY_URL`: Target Galaxy instance URL (example: `https://usegalaxy.org`)
- `GALAXY_API_KEY`: Galaxy API key (example: `<your-galaxy-api-key>`)
- optional environment variables:
- `GALAXY_MCP_TRANSPORT`: Transport mode (stdio or streamable-http) (example: `stdio`)
- `GALAXY_MCP_PUBLIC_URL`: Public base URL for OAuth redirects (HTTP mode) (example: `<your-public-url>`)
- `GALAXY_MCP_SESSION_SECRET`: Session secret for HTTP/OAuth mode (example: `<your-session-secret>`)
Note: MCP for Galaxy bioinformatics platform. Supports both stdio (local, API key auth) and HTTP (remote, OAuth) transports.
Add this MCP server to my current client's config in the correct format for you. If you need secrets or credentials I haven't provided, ASK me — do not invent values or leave raw placeholders. After adding it, tell me how to verify the server is connected.GALAXY_URLrequiredTarget Galaxy instanceGALAXY_API_KEYrequiredAPI key for Galaxy accessGALAXY_MCP_PUBLIC_URLrequiredPublic base URL for OAuth redirectsGALAXY_MCP_SESSION_SECRETrequiredSecret for session management