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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 not on your PATH, use the absolute path to the binary (e.g. ~/.local/bin/biomcp).

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)

Current builds do not discover a browsable biomcp://skill/<slug> catalog because no embedded use-case files ship. Resource discovery still gives agent clients a stable entry point 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.