PAGA Remote Tool (MCP Server)

Serves PAGA (Partition-based Graph Abstraction; Wolf et al., Genome Biology 2019) as a ToolUniverse remote tool: run_paga_trajectory — estimates connectivity between single-cell clusters and reports the strongest cluster pairs (the trajectory backbone).

Served remotely (not bundled) because PAGA pulls in scanpy + anndata + igraph + leidenalg. Computation is cheap once a neighbors graph exists; if one is absent the tool log-normalizes, runs PCA, and builds neighbors before sc.tl.paga.

Deploy

pip install -r requirements.txt          # scanpy + igraph + leidenalg
python paga_tool.py                        # starts the MCP server on 127.0.0.1:8022

Inputs are referenced by adata_path (a server-accessible .h5ad whose obs carries the requested cluster_key), since single-cell matrices are large. The cluster x cluster connectivity matrix returned is small and bounded. Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse

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