setuplisted

# ENCODE Toolkit Setup ## When to Use - User needs help installing or configuring the ENCODE Toolkit MCP server - User is getting connection errors or server startup failures - User asks "how do I set up ENCODE?" or "install ENCODE toolkit" - User needs to configure ENCODE credentials for restricted data access - User wants to verify their ENCODE server connection is working - User is setting up a new environment and needs the ENCODE plugin Help the user set up the ENCODE Toolkit server. The server connects Claude to the ENCODE Project genomics database — the largest public catalog of functional genomic elements with 8,000+ experiments across 50+ assay types. ## Installation The ENCODE Toolkit server is installed via `uvx` (recommended) or `pip`: ### For Claude Code (CLI) ```bash claude mcp add encode -- uvx encode-toolkit ``` ### For Claude Desktop Add to `claude_desktop_config.json`: - **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json` - **Windows**: `%APPDATA%\Claude\claude_desktop_config.json` ```json { "mcpServers": { "encode": { "command": "uvx", "args": ["encode-toolkit"] } } } ``` Then restart Claude Desktop. ### For VS Code (Claude Extension) Add to your VS Code `settings.json` (Ctrl/Cmd + Shift + P → "Preferences: Open Settings (JSON)"): ```json { "claude.mcpServers": { "encode": { "command": "uvx", "args": ["encode-toolkit"] } } } ``` ### For Cursor Add to `.cursor/mcp.json` in you