Dependencies¶

Start the AnyVar HTTP API¶

The MCP server uses AnyVar's HTTP API to register and retrieve variants. Follow AnyVar's setup instructions to start the HTTP API. Keep it running while you use the MCP tools.

AnyVar compatibility¶

This MCP server targets AnyVar commit ec3c765. Other versions may return different responses or lack required endpoints. Check your service's version at /service-info before using the examples.

Check the AnyVar HTTP API¶

Follow these steps to check that the AnyVar HTTP API is running correctly and can register a variant.

Set ANYVAR_API_URL to your service's base URL. Run these commands in the same terminal:

export ANYVAR_API_URL="http://localhost:8000"

Request service information:

curl --fail-with-body "${ANYVAR_API_URL%/}/service-info" \
  | python3 -m json.tool --indent 2

Expected response excerpt:

{
  "id": "org.biocommons.anyvar",
  "name": "AnyVar",
  "type": {
    "group": "org.biocommons",
    "artifact": "anyvar",
    "version": "1.0.1.dev196+gec3c7651b"
  }
}

The full response also includes service metadata, supported data standards, and dependency information. Check the version against the supported AnyVar commit.

Ensure AnyVar service is running

If the request fails, check the URL and that the service is running. Open the service's base URL in a browser to view its API documentation.

Register a variant¶

Register a sample variant to check processing and storage:

curl --fail-with-body --request PUT "${ANYVAR_API_URL%/}/variation" \
  --header 'Content-Type: application/json' \
  --data '{"definition": "NC_000010.11:g.87894077C>T"}' \
  | python3 -m json.tool --indent 2

Expected registration response:

{
  "input_variation": {
    "definition": "NC_000010.11:g.87894077C>T",
    "assembly_name": "GRCh38"
  },
  "messages": [],
  "object": {
    "id": "ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU",
    "type": "Allele",
    "digest": "K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU",
    "location": {
      "id": "ga4gh:SL.01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy",
      "type": "SequenceLocation",
      "digest": "01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy",
      "sequenceReference": {
        "type": "SequenceReference",
        "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB"
      },
      "start": 87894076,
      "end": 87894077
    },
    "state": {
      "type": "LiteralSequenceExpression",
      "sequence": "T"
    }
  },
  "object_id": "ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU"
}

Return to the quickstart to install and connect the MCP server.