Skip to main content
Glama
hlydecker

UCSC Genome Browser MCP Server

by hlydecker
OverviewSchemaRelated ServersScoreDiscussions
Python
Remote

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
NameRequiredDescriptionDefault
genomeNoSpecific genome to test for existence (optional)
max_itemsNoMaximum number of items to return (default: 1000000)

Implementation Reference

  • ucsc-genome-mcp.py:362-368 (handler)
    Handler implementation for the 'list_genark_genomes' tool. It extracts parameters from arguments, maps 'max_items' to 'maxItemsOutput', builds the API URL for the /list/genarkGenomes endpoint, and fetches the data using make_api_request.
    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)
    Registration of the 'list_genark_genomes' tool in the list_tools() decorator, defining its name, description, and input schema.
    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 definition for the 'list_genark_genomes' tool, specifying parameters for genome (optional string) and max_items (optional 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)"
        }
    }
}

Tool Definition Quality

B3.1/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden. It mentions listing genomes and testing existence, but doesn't disclose behavioral traits such as whether this is a read-only operation, potential rate limits, authentication needs, or what happens when testing for a non-existent genome. The description is minimal and lacks critical operational details.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise with two sentences that directly state the tool's functions. It's front-loaded with the primary purpose and includes an additional capability without unnecessary details. However, it could be slightly more structured by separating the listing and testing functions more clearly.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the complexity of genome listing/testing, lack of annotations, and no output schema, the description is incomplete. It doesn't explain return values, error handling, or how results are formatted. For a tool with 2 parameters and no structured safety hints, more context is needed to guide effective use.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents both parameters ('genome' and 'max_items') fully. The description adds marginal value by implying that 'genome' is used for testing existence, but doesn't provide additional semantics beyond what the schema states. Baseline 3 is appropriate as the schema does the heavy lifting.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: 'List UCSC Genome Browser database genomes from assembly hub host (GenArk)' with the specific action 'list' and resource 'genomes'. It also mentions an alternative function 'test for existence of a specific genome', which adds clarity. However, it doesn't explicitly differentiate from sibling tools like 'list_ucsc_genomes' or 'list_hub_genomes', which appear similar.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage by stating the tool can 'list' genomes and 'test for existence', but it doesn't provide explicit guidance on when to use this tool versus alternatives like 'list_ucsc_genomes' or 'search_genome'. No exclusions or prerequisites are mentioned, leaving usage context somewhat vague.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/hlydecker/ucsc-genome-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server