Add BioMCP to your MCP client¶

Use this page after installing BioMCP to connect the local biomcp serve stdio server to your MCP client.

Install biomcp-cli, not biomcp

The PyPI package for this project is biomcp-cli. It installs the biomcp binary used below. Do not run pip install biomcp; that PyPI package is unrelated to this project.

uv tool install biomcp-cli
biomcp --version

Fast path: generate the client config¶

BioMCP can print copy-paste setup for the supported local stdio clients:

biomcp mcp-config --client codex
biomcp mcp-config --client claude-desktop
biomcp mcp-config --client claude-code
biomcp mcp-config --client cursor
biomcp mcp-config --client cline
biomcp mcp-config --client vscode
biomcp mcp-config --client json

If your MCP client cannot see the same shell PATH where biomcp is installed, add --absolute-path:

biomcp mcp-config --client claude-desktop --absolute-path

The sections below are static fallbacks you can copy directly.

Codex¶

Generate the command:

biomcp mcp-config --client codex

Or add the server directly:

codex mcp add biomcp -- biomcp serve

Claude Code¶

For Claude Code, prefer the BioMCP plugin marketplace. Install the biomcp binary first, then run these Claude Code slash commands:

/plugin marketplace add genomoncology/biomcp
/plugin install biomcp@biomcp

The plugin wires Claude Code to the local stdio MCP server with biomcp serve. If you need manual JSON instead, generate it with:

biomcp mcp-config --client claude-code

Claude Desktop¶

When available in your Claude Desktop build, install BioMCP from the Anthropic Directory or MCPB extension flow. For a local manual setup, generate the JSON:

biomcp mcp-config --client claude-desktop

Then add this server entry to your Claude Desktop config:

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Restart Claude Desktop after changing the config.

Cursor¶

Generate the Cursor config:

biomcp mcp-config --client cursor

Or add this to your Cursor MCP config:

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Cline¶

Generate the Cline config:

biomcp mcp-config --client cline

Or add this server to Cline's MCP settings:

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

VS Code¶

Generate the VS Code config:

biomcp mcp-config --client vscode

Or add this server to .vscode/mcp.json in your workspace, or to the file VS Code opens with MCP: Open User Configuration. VS Code reads servers here, not the mcpServers key the other clients use — a snippet under the wrong key is valid JSON and is then silently ignored, so the server never shows up.

{
  "servers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Generic MCP JSON¶

Use the generic JSON form for any stdio MCP client that accepts an mcpServers object:

biomcp mcp-config --client json

Static fallback:

{
  "mcpServers": {
    "biomcp": {
      "command": "biomcp",
      "args": ["serve"]
    }
  }
}

Validate before connecting¶

Run quick local checks before restarting your client:

biomcp --version
biomcp health --apis-only

If the client still cannot start BioMCP, regenerate its config with --absolute-path and paste the result into the client settings.