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mcp/harbor
Gemini CLI

pathway commons mcp for Gemini CLI

io.github.mrfentmen/pathway-commons-mcp

Pathway Commons graph search: find pathways, proteins and complexes by name

client:Gemini CLI transport:stdio runtime:npm

Install pathway commons mcp in Gemini CLI

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

{
  "mcpServers": {
    "pathway-commons-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@mrfentmen/pathway-commons-mcp"
      ]
    }
  }
}

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

pathway commons mcp in other clients

pathway commons mcp MCP server