Cognee MCP Server for AI Code Analysis & Development

cognee‑mcp - Run cognee’s memory engine as a Model Context Protocol server

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Build memory for Agents and query from any client that speaks MCP – in your terminal or IDE.

✨ Features

SSE & stdio transports – choose real‑time streaming --transport sse or the classic stdio pipe
Integrated logging – all actions written to a rotating file (see get_log_file_location()) and mirrored to console in dev
Local file ingestion – feed .md, source files, Cursor rule‑sets, etc. straight from disk
Background pipelines – long‑running cognify & codify jobs spawn off‑thread; check progress with status tools
Developer rules bootstrap – one call indexes .cursorrules, .cursor/rules, AGENT.md, and friends into the developer_rules nodeset
Prune & reset – wipe memory clean with a single prune call when you want to start fresh

Please refer to our documentation here for further information.

🚀 Quick Start

Clone cognee repo

git clone https://github.com/topoteretes/cognee.git

Navigate to cognee-mcp subdirectory
```
cd cognee/cognee-mcp
```
Install uv if you don't have one
```
pip install uv
```
Install all the dependencies you need for cognee mcp server with uv
```
uv sync --dev --all-extras --reinstall
```
Activate the virtual environment in cognee mcp directory
```
source .venv/bin/activate
```
Set up your OpenAI API key in .env for a quick setup with the default cognee configurations
```
LLM_API_KEY="YOUR_OPENAI_API_KEY"
```
Run cognee mcp server with stdio (default)
```
python src/server.py
```
or stream responses over SSE
```
python src/server.py --transport sse
```

You can do more advanced configurations by creating .env file using our template. To use different LLM providers / database configurations, and for more info check out our documentation.

🐳 Docker Usage

If you’d rather run cognee-mcp in a container, you have two options:

Build locally

Make sure you are in /cognee root directory and have a fresh .env containing only your LLM_API_KEY (and your chosen settings).

Remove any old image and rebuild:

docker rmi cognee/cognee-mcp:main || true
docker build --no-cache -f cognee-mcp/Dockerfile -t cognee/cognee-mcp:main .

Run it:

docker run --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main

Pull from Docker Hub (no build required):

# With your .env file
docker run --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main

💻 Basic Usage

The MCP server exposes its functionality through tools. Call them from any MCP client (Cursor, Claude Desktop, Cline, Roo and more).

Available Tools

cognify: Turns your data into a structured knowledge graph and stores it in memory
codify: Analyse a code repository, build a code graph, stores it in memory
search: Query memory – supports GRAPH_COMPLETION, RAG_COMPLETION, CODE, CHUNKS, INSIGHTS
prune: Reset cognee for a fresh start
cognify_status / codify_status: Track pipeline progress

Remember – use the CODE search type to query your code graph. For huge repos, run codify on modules incrementally and cache results.

IDE Example: Cursor

After you run the server as described in the Quick Start, create a run script for cognee. Here is a simple example:

#!/bin/bash
export ENV=local
export TOKENIZERS_PARALLELISM=false
export EMBEDDING_PROVIDER="fastembed"
export EMBEDDING_MODEL="sentence-transformers/all-MiniLM-L6-v2"
export EMBEDDING_DIMENSIONS=384
export EMBEDDING_MAX_TOKENS=256
export LLM_API_KEY=your-OpenAI-API-key
uv --directory /{cognee_root_path}/cognee-mcp run cognee

Remember to replace your-OpenAI-API-key and {cognee_root_path} with correct values.

Install Cursor and navigate to Settings → MCP Tools → New MCP Server
Cursor will open mcp.json file in a new tab. Configure your cognee MCP server by copy-pasting the following:
```
{
  "mcpServers": {
    "cognee": {
      "command": "sh",
      "args": [
        "/{path-to-your-script}/run-cognee.sh"
      ]
    }
  }
}
```
Remember to replace {path-to-your-script} with the correct value of the path of the script you created in the first step.

That's it! You can refresh the server from the toggle next to your new cognee server. Check the green dot and the available tools to verify your server is running.

Now you can open your Cursor Agent and start using cognee tools from it via prompting.

Development and Debugging

Debugging

To use debugger, run: bash mcp dev src/server.py

Open inspector with timeout passed: http://localhost:5173?timeout=120000

To apply new changes while developing cognee you need to do:

poetry lock in cognee folder
uv sync --dev --all-extras --reinstall
mcp dev src/server.py

Development

In order to use local cognee:

Uncomment the following line in the cognee-mcp pyproject.toml file and set the cognee root path.
```
#"cognee[postgres,codegraph,gemini,huggingface,docs,neo4j] @ file:/Users/<username>/Desktop/cognee"
```
Remember to replace file:/Users/<username>/Desktop/cognee with your actual cognee root path.
Install dependencies with uv in the mcp folder
```
uv sync --reinstall
```

Code of Conduct

We are committed to making open source an enjoyable and respectful experience for our community. See CODE_OF_CONDUCT for more information.

Cognee