Agent skill · mims-harvard
setup-monocle3-remote-tool
Set up, launch, validate, and troubleshoot the Monocle 3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
What it needs
About 4k tokens when loaded.
What this skill does
Set up Monocle 3 as a remote tool Validation status (2026-08-16): R 4.4.3/Monocle3 1.4.27, loopback discovery, and two deterministic 240-cell calls passed with finite pseudotime for all cells; both disclosed the acyclic fallback after the upstream loop-closing bug. Public publication, cross-user isolation, representative biology, broad concurrency, and recovery remain incomplete. 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 only; R spatial dependencies can require substantial RAM. 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 monocle3 ~~~ 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/monocle3 . .venvs/monocle3/bin/activate python -m pip install --upgrade pip python -m pip install -e . python -m pip install -r src/tooluniverse/remote/monocle3/requirements.txt Rscript -e 'install.packages(c("BiocManager","remotes","Matrix","jsonlite")); BiocManager::install(c("SingleCellExperiment","batchelor","leidenbase","ggrastr")); remotes::installgithub("cole-trapnell-lab/monocle3")' ~~~ Package/network-dependent commands must be rerun in a clean environment before marking this skill complete. Obtain credentials, data, and model weights Set TOOLUNIVERSEREMOTEDATAROOT and optionally RSCRIPTBIN. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills mims-harvard/setup-monocle3-remote-tool