Scrublet Remote Tool (MCP Server)

Serves Scrublet (Wolock et al., Cell Systems 2019) — single-cell RNA-seq doublet detection — as a ToolUniverse remote tool: run_scrublet_doublets (per-cell doublet scores + boolean predictions).

Served remotely (not bundled) because it pulls in the scanpy/anndata single-cell stack plus scikit-image for the KNN/UMAP machinery. Scrublet operates on raw counts, not normalized/log-transformed data.

Deploy

pip install -r requirements.txt          # scanpy + scikit-image + anndata
python scrublet_tool.py                    # starts the MCP server on 127.0.0.1:8015

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

Register in ToolUniverse

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