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Claude Desktop (MCP) Setup

BioMCP can run as an MCP server over stdio. If your Claude Desktop build offers the Anthropic Directory, install BioMCP there first. Use the JSON config below when you want a local/manual setup.

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:

  • seven read-only tools: biomcp, search, get, variant_normalize_car, variant_erepo, gene_cspec, and variant_articles
  • one help resource (biomcp://help)
  • one markdown resource per embedded BioMCP worked example (biomcp://skill/<slug>)

Resource discovery gives agent clients both the overview entry point and the worked-example catalog before execution.

Prefer the bounded typed tools. Use biomcp only as the raw read-only escape hatch, beginning with biomcp list for compact command discovery. CI measures the real local tools/list response with uv run --no-sync python scripts/measure-mcp-tools.py and rejects catalogs over 22,600 UTF-8 bytes or 5,800 cl100k_base tokens; biomcp mcp tools prints the same catalog as a JSON array. The 22,600-byte / 5,800-token CI budget applies to the 0.9.0 released build. Exact current counts belong to that executable measurement rather than hand-copied documentation.

Operational tips

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