UCSC Genome Browser MCP Server

Instructions

Implementation Reference

• ucsc-genome-mcp.py:384-391 (handler)

  Handler logic for the 'list_tracks' tool: constructs parameters from arguments (genome, hub_url, track_leaves_only) and makes an API request to the UCSC Genome Browser's /list/tracks endpoint.

  elif name == "list_tracks":
      params = {
          "genome": arguments["genome"],
          "hubUrl": arguments.get("hub_url"),
          "trackLeavesOnly": 1 if arguments.get("track_leaves_only") else None
      }
      url = build_api_url("/list/tracks", params)
      result = await make_api_request(url)

• ucsc-genome-mcp.py:167-188 (registration)

  Registration of the 'list_tracks' tool in the MCP server's tool list, defining its name, description, and input schema.

  Tool(
      name="list_tracks",
      description="List all data tracks available in a specified hub or UCSC database genome.",
      inputSchema={
          "type": "object",
          "properties": {
              "genome": {
                  "type": "string",
                  "description": "Genome assembly name"
              },
              "hub_url": {
                  "type": "string",
                  "description": "URL of track/assembly hub (optional, required with genome for hub tracks)"
              },
              "track_leaves_only": {
                  "type": "boolean",
                  "description": "Only show tracks without composite container information"
              }
          },
          "required": ["genome"]
      }
  ),

• ucsc-genome-mcp.py:170-187 (schema)

  Input schema definition for the 'list_tracks' tool, specifying parameters: genome (required), hub_url (optional), track_leaves_only (optional).

  inputSchema={
      "type": "object",
      "properties": {
          "genome": {
              "type": "string",
              "description": "Genome assembly name"
          },
          "hub_url": {
              "type": "string",
              "description": "URL of track/assembly hub (optional, required with genome for hub tracks)"
          },
          "track_leaves_only": {
              "type": "boolean",
              "description": "Only show tracks without composite container information"
          }
      },
      "required": ["genome"]
  }