Agent skill · mims-harvard
setup-celltypist-remote-tool
Set up, launch, validate, and troubleshoot the CellTypist ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
What it needs
About 5k tokens when loaded.
What this skill does
Set up CellTypist as a remote tool Validation status (2026-08-16): working CPU deployment. The live MCP call annotated 80 cells from the official CellTypist sample and completed majority voting. A converted data-only model produced the same 80 labels and probabilities as the digest-pinned upstream model (maximum probability delta 0.0). This is runtime equivalence evidence, not an annotation-accuracy benchmark. Authenticated private Platform import and owner testing passed on 2026-08-16; public publication and independent-caller authorization/isolation remain untested. Prerequisites Run from the ToolUniverse repository root on Linux with Python 3.12.3. CPU is sufficient for the validated model and sample. Keep provider data, weights, caches, and credentials outside Git. Bind to loopback. A non-loopback bind requires TOOLUNIVERSEAPITOKEN; never put it in arguments or results. Run the standard-library contract check before downloading large dependencies: ~~~bash python scripts/remotevalidation/setupskillpreflight.py --implementation celltypist ~~~ After exporting provider resources, add --check-provider-env. After the server starts, add --live to verify the exact MCP tool set without running the model. Before sharing, add --check-connect-prereqs; this reports only whether a key is set and never prints its value. Create an isolated environment ~~~bash python3 -m venv .venvs/celltypist . .venvs/celltypist/bin/activate python -m pip install --upgrade pip python -m pip install -e . python -m pip install -r src/tooluniverse/remote/celltypist/requirements.txt ~~~ Package/network-dependent commands must be rerun in a clean environment before marking this skill complete. Obtain data and provision a safe model Set TOOLUNIVERSEREMOTEDATAROOT to the provider-owned directory containing normalized .h5ad inputs. Download the model only from the official CellTypist host and verify its digest independently. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills mims-harvard/setup-celltypist-remote-tool