io.github.cyanheads/ensembl-mcp-server MCP Server

io.github.cyanheads/ensembl-mcp-server

Repository Registry

What is the io.github.cyanheads/ensembl-mcp-server MCP server?

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

How to install io.github.cyanheads/ensembl-mcp-server

Copy-paste configuration for popular MCP clients.

transport: stdio

Config generated by PluginBench — verify against the source before use.

Environment / auth

ENSEMBL_BASE_URL
Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.
MCP_LOG_LEVEL
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').
MCP_HTTP_HOST
The hostname for the HTTP server.
MCP_HTTP_PORT
The port to run the HTTP server on.
MCP_HTTP_ENDPOINT_PATH
The endpoint path for the MCP server.
MCP_AUTH_MODE
Authentication mode to use: 'none', 'jwt', or 'oauth'.

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "bun",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<YOUR_ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>",
        "MCP_HTTP_HOST": "<YOUR_MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<YOUR_MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<YOUR_MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<YOUR_MCP_AUTH_MODE>"
      }
    }
  }
}

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