Local MCP server

The smarts CLI includes a local MCP server over stdio. Clients that can launch a local process — Claude Desktop, Claude Code, Cursor, Windsurf, and the Gemini CLI — spawn it as a subprocess. It reuses your CLI credentials, so there's no extra login.

1. Install & log in

Install the CLI and authenticate once:

brew install smartsbio/tap/smarts
smarts login

2. Register it with your client

The CLI can write the right config for you:

smarts mcp install claude        # Claude Desktop
smarts mcp install claude-code   # Claude Code
smarts mcp install cursor        # Cursor
smarts mcp install windsurf      # Windsurf
smarts mcp install gemini        # Gemini CLI

Then restart the client. smarts.bio appears as an MCP server with all of its tools.

Manual configuration

Prefer to edit the config yourself? Add this to your client's MCP config (for Claude Desktop, claude_desktop_config.json):

{
  "mcpServers": {
    "smarts": {
      "command": "smarts",
      "args": ["mcp", "serve"]
    }
  }
}

Run it directly

You can also start the server by hand to test it:

Tools

The local server exposes the same tool set as the hosted one — see the full tool list. When a tool's workspace_id is omitted, it uses your CLI's current workspace (smarts workspace use). For reproducible pipelines:

• smarts_list_pipelines — built-in pipelines plus the ones saved in the workspace
• smarts_get_pipeline — inputs and steps of a built-in (pipeline_id) or saved (spec_file) pipeline
• smarts_run_pipeline — run by exactly one of pipeline_id or spec_file
• smarts_save_pipeline — save a finished run as a pipeline spec