MotherDuck MCP Server

Overview

A Model Context Protocol (MCP) server implementation that provides read-only access to MotherDuck databases. Supports database and schema-level access control.

Tools

• motherduck-list-tables

  • Lists available tables in the database
  • Optional filter by database name
  • Example: {"database": "compound_pipeline"}

• motherduck-describe-table

  • Shows table structure (columns, types, nullability)
  • Requires full table name: database.schema.table
  • Example: {"table_name": "compound_pipeline.oncology_all.genetarget"}

• motherduck-query

  • Executes read-only SQL queries
  • Requires fully qualified table names
  • Example: {"sql": "SELECT * FROM compound_pipeline.oncology_all.genetarget LIMIT 5"}

Configuration

Required Environment Variables

• MOTHERDUCK_TOKEN: Your MotherDuck authentication token

Optional Environment Variables

• ALLOWED_DATASETS: Restrict access to specific databases/schemas
  • Format: database or database.schema (comma-separated)
  • Examples:

    # Full database access
    ALLOWED_DATASETS=compound_pipeline
    
    # Single schema access
    ALLOWED_DATASETS=compound_pipeline.oncology_all
    
    # Multiple schemas
    ALLOWED_DATASETS=compound_pipeline.oncology_all,compound_pipeline.clinicaltrials

Usage with Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "MOTHERDUCK-MCP": {
      "command": "uv",
      "args": ["-m", "mcp_server_motherduck"],
      "env": {
        "MOTHERDUCK_TOKEN": "YOUR_TOKEN",
        "ALLOWED_DATASETS_MOTHERDUCK": "YOUR_ALLOWED_DATASETS"  // Optional
      }
    }
  }
}

License

GNU General Public License v3.0 (GPL-3.0)