Borzoi Remote Tool (MCP Server)

Serves Borzoi (Linder et al., Nature Genetics 2025) — sequence → RNA-seq/multi-omic coverage prediction, the successor to Enformer — as ToolUniverse remote tools: run_borzoi_predict and run_borzoi_variant_effect.

Served remotely (not bundled) because it needs PyTorch + ~0.8 GB of weights per replicate (johahi/borzoi-replicate-{0..3}) and is GPU-recommended.

Deploy

pip install -r requirements.txt          # torch + borzoi-pytorch
python borzoi_tool.py                      # starts the MCP server on 127.0.0.1:8012

Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse

Tool definitions: src/tooluniverse/data/remote_tools/borzoi_tools.json (type: RemoteTool). Connect via the standard MCPAutoLoaderTool/server_url mechanism. First call lazily downloads and caches the weights.