cBioPortal MCP Server

WARNING ⚠️: This is still under construction

A wrapper around the mcp-clickhouse server adding a cBioPortal-specific system prompt.

Installation

# Navigate to the project directory
cd cbioportal-mcp

# Create a virtual environment
python -m venv venv

# Activate the virtual environment
# On macOS/Linux:
source venv/bin/activate
# On Windows:
# venv\Scripts\activate

# Upgrade pip
pip install --upgrade pip

# Install the package in development mode
pip install -e .

# Or install with development dependencies
pip install -e "."

Configuration

Set the same environment variables used by mcp-clickhouse:

export CLICKHOUSE_HOST=your-clickhouse-host
export CLICKHOUSE_PORT=9000
export CLICKHOUSE_USER=your-username
export CLICKHOUSE_PASSWORD=your-password
export CLICKHOUSE_DATABASE=your-cbioportal-database  # e.g., cgds_public_2025_06_24
export CLICKHOUSE_SECURE=true  # or false for insecure connections
export CLICKHOUSE_MCP_SERVER_TRANSPORT=stdio # or http or sse

Development

Inspecting the Server with MCP Inspector

To connect to the MCP server and see requests and replies, use MCP Inspector. You can run it with:

fastmcp dev src/cbioportal_mcp/server.py

Running the Server

# For development
python -m cbioportal_mcp.server

# Or using the installed script
cbioportal-mcp

Running in Docker

# Build the image
docker build -t cbioportal-mcp -f docker/Dockerfile .
docker run -i -p 8000:8000 cbioportal-mcp

License

MIT License - see LICENSE file for details.

Related Projects

• cBioPortal - The main cBioPortal platform
• mcp-clickhouse - ClickHouse MCP server