A fastmcp-based tool for writing prompts against data in the NMDC database.
You can install the package from source using uv:
uv syncYou can use the CLI:
nmdc-mcpOr import in your Python code: # TODO incorrect instructions
from nmdc_mcp.main import create_mcp
mcp = create_mcp()
mcp.run()Or utilize the nmdc_mcp.client. This client uses OpenAI API and assumes you have API_KEY set in a .env file in the root directory of this repo. The BASE_URL and MODEL are also customizable in .env. For PNNL staff that want to run via this client - the BASE_URL and MODEL are specific. Contact Olivia Hess if you need help setting these values up.
uv run 'path/to/nmdc_mcp/client.py' 'path/to/nmdc_mcp/main.py'Or using python
python 'path/to/nmdc_mcp/client.py' 'path/to/nmdc_mcp/main.py'# Clone the repository
git clone https://github.com/microbiomedata/nmdc-mcp.git
cd nmdc-mcp
# Install development dependencies
make devThe project uses a comprehensive Makefile for development tasks:
# Run all development checks (tests, formatting, linting, type checking)
make all
# Individual commands
make dev # Install development dependencies
make test-coverage # Run tests with coverage
make format # Format code with black
make lint # Lint with ruff
make mypy # Type checking
make deptry # Check for unused dependencies
make build # Build package# Run all tests with coverage
make test-coverage
# Run specific test types
make test-unit # Unit tests only
make test-integration # Integration tests
make test-real-api # Tests against real NMDC API
make test-mcp # Test MCP protocolAdd to ~/Library/Application Support/Claude/claude_desktop_config.json:
{
"mcpServers": {
"nmdc-mcp": {
"command": "uvx",
"args": ["nmdc-mcp"]
}
}
}claude mcp add -s project nmdc-mcp uvx nmdc-mcpgoose session --with-extension "uvx nmdc-mcp"MIT