How to Start the MCP Server for Claude Code Integration with Code-Graph-RAG

Run cgr mcp-server after installing the package and starting the Docker services with cgr daemon up, then register the server with Claude Code using the claude mcp add command to enable AI-powered codebase queries.

The MCP (Model-Context Protocol) server bridges Claude Code and the Code-Graph-RAG knowledge graph, allowing AI agents to query your codebase structure and semantics through deterministic tools. This integration transforms Claude Code into an intelligent coding assistant that understands cross-file relationships stored in Memgraph. According to the vitali87/code-graph-rag source code, the server runs as a stdio-based process that exposes graph query capabilities via the MCP protocol.

Prerequisites: Installation and Docker Setup

Before starting the MCP server, you must install the Code-Graph-RAG package and spin up the required backend services. The system relies on Memgraph for the knowledge graph and Qdrant for vector storage, both containerized via Docker.

Installing the Package

Install the tool using uv (recommended) or pipx to place the cgr executable on your PATH:

# Via uv (recommended)

uv tool install "code-graph-rag[treesitter-full,semantic]"

# Or via pipx

pipx install "code-graph-rag[treesitter-full,semantic]"

The [treesitter-full,semantic] extras ensure full language parsing capabilities required for graph construction.

Starting the Backend Services

Launch the Docker containers for Memgraph and Qdrant:

cgr daemon up

This command initializes the graph database where your codebase structure will be indexed.

Starting the MCP Server

Once dependencies are running, you can start the server using either the installed binary or by running directly from source.

From Binary Installation

If you installed via uv or pipx, simply execute:

cgr mcp-server

This starts a long-running stdio process that listens for MCP protocol messages and exposes tools defined in codebase_rag/mcp/tools.py.

From Source Checkout

When developing or running from a local clone of the vitali87/code-graph-rag repository:

git clone https://github.com/vitali87/code-graph-rag.git
cd code-graph-rag
uv sync

# Start the server via uv

uv run --directory . code-graph-rag mcp-server

The entry point for this command is defined in codebase_rag/cli.py around line 950, where the mcp_server Typer command initializes the stdio server using the mcp library.

Registering the Server with Claude Code

After starting the server, register it as an MCP provider in Claude Code. This requires specifying environment variables for the target repository and LLM configuration.

claude mcp add --transport stdio code-graph-rag \
  --env TARGET_REPO_PATH=/absolute/path/to/your/project \
  --env CYPHER_PROVIDER=openai \
  --env CYPHER_MODEL=gpt-5.6-luna \
  --env CYPHER_API_KEY=your-api-key \
  -- code-graph-rag mcp-server

Important limitation: Only one repository can be indexed per MCP instance. When you change TARGET_REPO_PATH to a new directory, the previous index is cleared automatically.

Verify the registration:

claude mcp list

You should see code-graph-rag listed among available MCP servers.

Architectural Overview and Key Files

Understanding the implementation helps troubleshoot integration issues and extend functionality.

CLI Entry Point

The mcp_server command is implemented in codebase_rag/cli.py. This function initializes the stdio transport and registers all available tools.

MCP Client Helper

For programmatic access outside Claude Code, codebase_rag/mcp/client.py contains the query_mcp_server function. This helper opens a temporary stdio client, sends JSON-RPC requests, and parses responses:

from codebase_rag.mcp.client import query_mcp_server

response = query_mcp_server("What functions call UserService.create_user?")
print(response["output"])

Tool Definitions

All deterministic tools exposed to Claude Code—such as list_projects, query_code_graph, and ask_agent—are defined in codebase_rag/mcp/tools.py. These tools connect to Memgraph via pymgclient to execute Cypher queries against the knowledge graph.

Summary

• Install the package using uv tool install or pipx install with the [treesitter-full,semantic] extras to get the cgr command
• Start services with cgr daemon up to launch Memgraph and Qdrant containers
• Launch the server using cgr mcp-server, which runs as a stdio process defined in codebase_rag/cli.py
• Register with Claude Code via claude mcp add, setting TARGET_REPO_PATH and CYPHER_* environment variables
• Query programmatically using the helper in codebase_rag/mcp/client.py when building external integrations

Frequently Asked Questions

What environment variables are required to start the MCP server for Claude Code?

The essential variables are TARGET_REPO_PATH (absolute path to the repository to index), CYPHER_PROVIDER (e.g., "openai"), CYPHER_MODEL (the specific model name), and CYPHER_API_KEY (your LLM API key). These are passed via the --env flags when running claude mcp add.

Can I index multiple repositories with one MCP server instance?

No, the architecture currently supports only one repository per MCP instance. When you point TARGET_REPO_PATH to a new directory, the previous graph data is cleared automatically. For multiple repositories, you must run separate MCP server instances with different configurations.

How do I verify that the MCP server is running correctly?

First, ensure cgr daemon up has started the Memgraph and Qdrant containers without errors. Then run claude mcp list after registration—you should see code-graph-rag in the output. You can also test the Python helper query_mcp_server from codebase_rag/mcp/client.py to verify stdio communication.

Where is the MCP server entry point defined in the source code?

The command implementation is located in codebase_rag/cli.py around line 950, within the mcp_server function. This Typer command sets up the stdio transport and wires the tools defined in codebase_rag/mcp/tools.py to handle incoming MCP requests.

{
  "mcpServers": {
    "instagit": {
      "command": "npx",
      "args": ["-y", "instagit@latest"]
    }
  }
}