scVI Remote Tool (MCP Server)

Serves scVI (Lopez et al., Nature Methods 2018; scvi-tools, Gayoso et al., Nature Biotechnology 2022) — probabilistic single-cell RNA-seq modeling — as ToolUniverse remote tools: run_scvi_integration (batch-corrected latent representation) and run_scvi_differential_expression.

Served remotely (not bundled) because scvi-tools pulls in PyTorch + Lightning + Pyro + scanpy. Small datasets train on CPU; large ones benefit from a GPU.

Deploy

pip install -r requirements.txt          # scvi-tools + scanpy
python scvi_tool.py                        # starts the MCP server on 127.0.0.1:8010

Inputs are referenced by adata_path (a server-accessible .h5ad of raw UMI counts), since single-cell matrices are large. Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse

Tool definitions: src/tooluniverse/data/remote_tools/scvi_tools.json (type: RemoteTool). Connect via the standard MCPAutoLoaderTool/server_url mechanism.