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Claude Desktop (MCP) Setup

BioMCP can run as an MCP server over stdio.

Add BioMCP server config

Use biomcp serve as the MCP command:

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

If BioMCP is inside a virtual environment, use the absolute path to that binary.

Validate before connecting Claude

biomcp --version
biomcp health --apis-only

Verify MCP-level behavior

When connected, clients should discover:

  • one tool: shell
  • one help resource (biomcp://help) and one resource per installed skill (biomcp://skill/<slug>)

Resource discovery gives agent clients structured entry points before execution.

Operational tips

  • Keep API keys in the client launch environment.
  • Restart Claude Desktop after config changes.
  • Prefer stable absolute paths in managed environments.