.mcp.json

{
  "mcpServers": {
    "ngs-app": {
      "command": "./start_server",
      "args": ["ngs_app_mcp"],
      "cwd": "./mcp",
      "startup_timeout_sec": 120,
      "env": {
        "PYTHONPATH": "."
      },
      "env_vars": [
        "CODEX_HOME",
        "NGS_ANALYSIS_WORKBENCH_STATE_DIR"
      ],
      "default_tools_approval_mode": "auto"
    },
    "ngs-analysis-workbench": {
      "command": "./start_server",
      "args": [],
      "cwd": "./mcp",
      "startup_timeout_sec": 120,
      "env": {
        "PYTHONPATH": "."
      },
      "env_vars": [
        "CODEX_HOME",
        "NGS_ANALYSIS_WORKBENCH_STATE_DIR"
      ],
      "default_tools_approval_mode": "auto",
      "tools": {
        "execute_plan": {
          "approval_mode": "prompt"
        }
      }
    },
    "ngs-compute": {
      "command": "./start_server",
      "args": ["ngs_compute_mcp"],
      "cwd": "./mcp",
      "startup_timeout_sec": 120,
      "env": {
        "PYTHONPATH": "."
      },
      "env_vars": [
        "CODEX_HOME",
        "NGS_ANALYSIS_WORKBENCH_STATE_DIR"
      ],
      "default_tools_approval_mode": "auto"
    }
  }
}