Set up Monocle 3 as a remote tool

Sharing this model for a user, not developing it? Follow the tooluniverse-share-computer guide; no ToolUniverse source checkout is needed. The model runs in its own Python environment, with its dependencies:

~/.local/bin/uv venv --python 3.12 ~/.tooluniverse/envs/monocle3
curl -fsSL -o ~/.tooluniverse/envs/monocle3-tooluniverse.txt https://connect.aiscientist.tools/install-requirements.txt
curl -fsSL -o ~/.tooluniverse/envs/monocle3-requirements.txt https://raw.githubusercontent.com/mims-harvard/ToolUniverse/main/src/tooluniverse/remote/monocle3/requirements.txt
~/.local/bin/uv pip install --python ~/.tooluniverse/envs/monocle3/bin/python -r ~/.tooluniverse/envs/monocle3-tooluniverse.txt -r ~/.tooluniverse/envs/monocle3-requirements.txt
~/.local/bin/tu remote check monocle3 --python ~/.tooluniverse/envs/monocle3/bin/python   # lists anything still missing
~/.local/bin/tu serve --allow monocle3 --python ~/.tooluniverse/envs/monocle3/bin/python --share --detach --name "<computer name>" --service https://tooluniverse-backend.onrender.com

If the check reports a missing environment variable (a data folder, a model cache, a provider key), set it in the same shell before tu serve; "Obtain credentials, data, and model weights" below says what each one is. The model reads only the variables it declares.

The rest of this guide is for developers working from the ToolUniverse source, and for diagnosing problems with this model.

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.