ENCODE Toolkit for Gemini CLI

io.github.ammawla/encode-toolkit

20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines

client:Gemini CLI transport:stdio runtime:npm

Install ENCODE Toolkit in Gemini CLI

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

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}

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