list_genark_genomes
Retrieve available genome assemblies from UCSC's GenArk database or verify if a specific genome exists for genomic analysis and research.
Instructions
List UCSC Genome Browser database genomes from assembly hub host (GenArk). Can also test for existence of a specific genome.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| genome | No | Specific genome to test for existence (optional) | |
| max_items | No | Maximum number of items to return (default: 1000000) |
Implementation Reference
- ucsc-genome-mcp.py:362-368 (handler)Handler for the 'list_genark_genomes' tool. Builds API request to '/list/genarkGenomes' endpoint with optional 'genome' and 'max_items' parameters, fetches data from UCSC GenArk host, and returns JSON response.elif name == "list_genark_genomes": params = { "genome": arguments.get("genome"), "maxItemsOutput": arguments.get("max_items") } url = build_api_url("/list/genarkGenomes", params) result = await make_api_request(url)
- ucsc-genome-mcp.py:113-129 (registration)Tool registration in list_tools(), including name, description, and input schema definition for 'list_genark_genomes'.Tool( name="list_genark_genomes", description="List UCSC Genome Browser database genomes from assembly hub host (GenArk). Can also test for existence of a specific genome.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Specific genome to test for existence (optional)" }, "max_items": { "type": "integer", "description": "Maximum number of items to return (default: 1000000)" } } } ),
- ucsc-genome-mcp.py:116-128 (schema)Input schema defining parameters for the 'list_genark_genomes' tool: optional genome (string) and max_items (integer).inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Specific genome to test for existence (optional)" }, "max_items": { "type": "integer", "description": "Maximum number of items to return (default: 1000000)" } } }
- ucsc-genome-mcp.py:27-37 (helper)Helper function build_api_url used by the handler to construct the UCSC API URL with semicolon-separated parameters.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 the handler to perform asynchronous HTTP GET request and parse JSON response.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()