mcp_config.yaml

# MCP Server Configuration for CodeAgent
# This file defines MCP servers and their tools for the LangGraph CodeAgent
# Supports both local (stdio) and remote (HTTP/WebSocket) MCP servers


mcp_servers:
  alphagenome:
    command: ["python", "AlphaGenome_mcp.py"]
    enabled: true
    description: "AlphaGenome MCP server for genomic analysis"

# mcp_servers:
#   # Remote MCP Server Example
#   alphagenome:
#     url: "https://alphagenome.fastmcp.app/mcp"
#     enabled: true
#     description: "AlphaGenome MCP server for genomic analysis"

    # Authentication options (optional)
    # auth:
    #   type: "bearer"  # or "api_key" or "basic"
    #   token: "${ALPHAGENOME_TOKEN}"  # Environment variable

    # SSL/TLS configuration (optional)
    # ssl:
    #   verify_ssl: true
    #   cert_file: "/path/to/client.crt"
    #   key_file: "/path/to/client.key"
    #   ca_file: "/path/to/ca.crt"

    # Connection timeouts (optional)
    # timeout:
    #   total: 30
    #   connect: 10
    #   read: 10

  # Example: Remote MCP Server with Authentication
  # remote_authenticated:
  #   url: "https://api.example.com/mcp"
  #   enabled: false
  #   description: "Authenticated remote MCP server"
  #   auth:
  #     type: "api_key"
  #     key: "${API_KEY}"
  #     header: "X-API-Key"
  #   timeout:
  #     total: 60
  #     connect: 15
  #     read: 30

  # Example: Custom Local Python MCP Server
  # custom_local_server:
  #   command: ["python", "path/to/your/custom_mcp_server.py"]
  #   enabled: false
  #   description: "Your custom local MCP server"
  #   env:
  #     API_KEY: "${YOUR_API_KEY}"
  #   tools:
  #     - biomni_name: custom_tool
  #       description: "Description of your custom tool"
  #       parameters:
  #         param1: {type: str, required: true, description: "Parameter description"}

# Additional Configuration Options:
#
# Authentication Types:
# - bearer: Uses Bearer token in Authorization header
# - api_key: Uses custom header for API key
# - basic: Uses Basic HTTP authentication
#
# Environment Variables:
# - Use ${VAR_NAME} syntax to reference environment variables
# - Useful for storing sensitive credentials outside config files
#
# Connection Features:
# - Automatic retry with exponential backoff
# - Health check monitoring
# - SSL/TLS certificate validation
# - WebSocket support for real-time communication
# - Connection pooling and timeout management