Ensembl MCP Server

by cyanheadsio.github.cyanheads/ensembl-mcp-serverv0.5.1

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

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Active1d ago

Install Ensembl MCP server

claude mcp add ensembl -- npx -y @cyanheads/ensembl-mcp-server

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project).

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Settings → Developer → Edit Config (claude_desktop_config.json), then restart.

{
  "servers": {
    "ensembl": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Add to .vscode/mcp.json in your workspace.

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json.

Configuration

Variable	Required	Secret	Description
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_TRANSPORT_TYPE	—	—	Selects the HTTP transport.
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'.