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mcp/harbor
Gemini CLI

BioMapper for Gemini CLI

io.github.trentleslie/biomapper

Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs.

client:Gemini CLI transport:stdio runtime:pypi

Install BioMapper in Gemini CLI

~/.gemini/settings.json · windows: %USERPROFILE%\.gemini\settings.json

Held in this page only — never stored, logged, or sent anywhere but back to your screen. 

{
  "mcpServers": {
    "biomapper": {
      "command": "uvx",
      "args": [
        "biomapper"
      ],
      "env": {
        "BIOMAPPER_MCP_ROOTS": "<BIOMAPPER_MCP_ROOTS>",
        "BIOMAPPER_API_KEY": "<BIOMAPPER_API_KEY>",
        "BIOMAPPER_BASE_URL": "<BIOMAPPER_BASE_URL>",
        "BIOMAPPER_MCP_HOME": "<BIOMAPPER_MCP_HOME>"
      }
    }
  }
}

Gemini expands $VAR and ${VAR} inside env values, so a secret can live in your shell rather than this file. Gemini CLI docs

BioMapper in other clients

BioMapper MCP server