mcp

atb mcp¶

Start MCP server for LLM integration

Synopsis¶

Start a Model Context Protocol (MCP) server over stdio or HTTP/SSE.

This allows LLMs like Claude and ChatGPT to query the AllTheBacteria database through structured tool calls.

The server exposes 5 tools: atb_query Search bacterial genomes by species, genus, quality, etc. atb_amr Query AMR resistance genes for a species atb_info Get all metadata for a specific sample accession atb_stats Database summary statistics atb_species_list List available species sorted by sample count

Usage with Claude Code: claude mcp add atb -- atb mcp --data-dir ~/atb/metadata/parquet

Usage with Claude Desktop (add to claude_desktop_config.json): { "mcpServers": { "atb": { "command": "atb", "args": ["mcp", "--data-dir", "/path/to/data"] } } }

Usage with ChatGPT / OpenAI API (HTTP/SSE mode): Start the server with --http, then configure ChatGPT with the SSE URL.

atb mcp [flags]

Examples¶

  # Start stdio server (for Claude Code, Cursor, Codex CLI)
  atb mcp --data-dir ~/atb/metadata/parquet

  # Start HTTP/SSE server (for ChatGPT, OpenAI API, remote clients)
  atb mcp --data-dir ~/atb/metadata/parquet --http :8080

  # ChatGPT: configure with URL http://your-host:8080/sse

  # Add to Claude Code
  claude mcp add atb -- atb mcp --data-dir ~/atb/metadata/parquet

Options¶

  -h, --help          help for mcp
      --http string   Start HTTP/SSE server on this address (e.g., :8080)

Options inherited from parent commands¶

      --config string     config file (default $HOME/.atb/config.toml)
      --data-dir string   directory for the local metadata index (default ~/.local/share/atb/data; override with $ATB_DATA_DIR)

mcp

atb mcp¶

Synopsis¶

Examples¶

Options¶

Options inherited from parent commands¶

SEE ALSO¶