UCSC Genome Browser MCP Server

Instructions

Implementation Reference

• ucsc-genome-mcp.py:375-382 (handler)

  Handler implementation for the 'list_files' tool. Constructs parameters from input arguments and makes an API request to the UCSC Genome Browser's /list/files endpoint.

  elif name == "list_files":
      params = {
          "genome": arguments["genome"],
          "format": arguments.get("format"),
          "maxItemsOutput": arguments.get("max_items")
      }
      url = build_api_url("/list/files", params)
      result = await make_api_request(url)

• ucsc-genome-mcp.py:144-166 (registration)

  Registration of the 'list_files' tool in the list_tools() function, including name, description, and input schema.

  Tool(
      name="list_files",
      description="List download files available for a specified UCSC genome assembly.",
      inputSchema={
          "type": "object",
          "properties": {
              "genome": {
                  "type": "string",
                  "description": "Genome assembly name (e.g., 'hg38', 'mm10')"
              },
              "format": {
                  "type": "string",
                  "enum": ["json", "text"],
                  "description": "Output format (default: json)"
              },
              "max_items": {
                  "type": "integer",
                  "description": "Maximum number of items to return"
              }
          },
          "required": ["genome"]
      }
  ),

• ucsc-genome-mcp.py:147-165 (schema)

  Input schema definition for the 'list_files' tool, specifying parameters like genome (required), format, and max_items.

  inputSchema={
      "type": "object",
      "properties": {
          "genome": {
              "type": "string",
              "description": "Genome assembly name (e.g., 'hg38', 'mm10')"
          },
          "format": {
              "type": "string",
              "enum": ["json", "text"],
              "description": "Output format (default: json)"
          },
          "max_items": {
              "type": "integer",
              "description": "Maximum number of items to return"
          }
      },
      "required": ["genome"]
  }

• ucsc-genome-mcp.py:27-37 (helper)

  Helper function build_api_url used by list_files handler to construct the API request URL.

  def build_api_url(endpoint: str, params: dict[str, Any]) -> str:
      """Build the complete API URL with parameters."""
      # Filter out None values
      filtered_params = {k: v for k, v in params.items() if v is not None}
      
      # Convert parameters to URL format (using semicolons as per UCSC API spec)
      if filtered_params:
          param_str = ";".join(f"{k}={v}" for k, v in filtered_params.items())
          return f"{BASE_URL}{endpoint}?{param_str}"
      return f"{BASE_URL}{endpoint}"

• ucsc-genome-mcp.py:39-45 (helper)

  Helper function make_api_request used by list_files handler to perform the HTTP GET request and parse JSON.

  async def make_api_request(url: str) -> dict[str, Any]:
      """Make an HTTP request to the UCSC API and return JSON response."""
      async with httpx.AsyncClient(timeout=30.0) as client:
          response = await client.get(url)
          response.raise_for_status()
          return response.json()