tutorials/examples/add_mcp_server/mcp_config.yaml

# MCP Server Config for Biomni

mcp_servers:
  # GitHub MCP Server (Docker approach - adding all tools)
  github:
    command: ["docker", "run", "-i", "--rm", "-e", "GITHUB_PERSONAL_ACCESS_TOKEN", "ghcr.io/github/github-mcp-server"]
    enabled: true
    description: "Official GitHub MCP server for repository and issue management"
    env:
      GITHUB_PERSONAL_ACCESS_TOKEN: "${GITHUB_TOKEN}"

  # Custom Local MCP Server - Only add tools necessary
  pubmed:
    command: ["python", "-m", "biomni.tool.example_mcp_tools.pubmed_mcp"]
    enabled: true
    tools:
      - biomni_name: search_pubmed
        description: "Search PubMed"
        parameters:
          query:        {type: str, required: true,  description: "PubMed search term"}
          max_results:  {type: int, required: false, default: 10, description: "Maximum number of hits"}
      - biomni_name: get_article_abstract
        description: "Fetch PubMed abstract"
        parameters:
          pmid: {type: str, required: true, description: "PubMed ID"}