scANVI Remote Tool (MCP Server)#

TOU validation and deployment status (2026-08-16)#

scANVI dependencies, GB10 execution, loopback discovery, and a bounded labeled/unlabeled annotation call passed with aligned predictions. Public publication, cross-user isolation, representative accuracy, 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.

  • Operation: run_scanvi_annotate

  • Start: python -m tooluniverse.remote.scanvi.scanvi_tool

  • Endpoint: http://127.0.0.1:8027/mcp

  • Provider configuration: set TOOLUNIVERSE_REMOTE_DATA_ROOT; labels_key and unlabeled_category must match the approved H5AD annotations.

  • TOU check: tu doctor --forward http://127.0.0.1:8027/mcp --json

  • Private relay: tu serve --share --forward http://127.0.0.1:8027/mcp --name validation-scanvi --workers 1

Non-loopback binding requires TOOLUNIVERSE_API_TOKEN; otherwise keep the server on loopback. The relay requires TOOLUNIVERSE_SERVICE_KEY. Public publication and independent-caller testing were not run.

New-user check: python scripts/remote_validation/setup_skill_preflight.py --implementation scanvi. Add --check-provider-env before launch, --live after launch, and --check-connect-prereqs before sharing. Live preflight checks exact MCP discovery only; it does not run or validate a model. The pinned relay SDK is not on PyPI and currently requires authorized GitHub repository access plus a configured SSH key, so a working local MCP server does not by itself prove that a new operator can share it.

The authenticated 2026-08-16 Platform matrix found all 30 private owner relays online and all 41 operations discoverable. This implementation was imported as unpublished owner draft(s), configured with a 120-second timeout, and invoked through /expert-sessions/{id}/test. Across the set, 38 unique operations passed return-schema and semantic validation; the three USPTO operations returned exact provider HTTP 403 and remain credential-blocked. Public publication, independent-caller authorization/isolation, broad saturation, and persistent supervision were not tested.

See the complete setup and verification guide.

Serves scANVI (Xu et al., Molecular Systems Biology 2021; scvi-tools, Gayoso et al., Nature Biotechnology 2022) — semi-supervised single-cell annotation / reference label transfer — as the ToolUniverse remote tool run_scanvi_annotate.

scANVI extends scVI: it pretrains scVI on raw UMI counts, then refines the model semi-supervised on the cells that already carry a known label, and predicts a cell type for every cell. Use it to transfer labels onto the unlabeled cells of a partially-annotated dataset.

Served remotely (not bundled) because scvi-tools pulls in PyTorch + Lightning + Pyro + scanpy. Small datasets train on CPU; large ones benefit from a GPU.

Authorize once, then share with one short command#

After installing this provider’s dependencies and the pinned Connect relay SDK, and exporting its required resources, run once per machine (and again after key rotation):

tu remote login
# Or import an existing protected 0600 file without sourcing it:
tu remote login --env-file /path/to/tooluniverse-service.env

Then each private share is:

tu remote share scanvi

By default, tu remote login requests a short-lived device code, opens the TU Platform approval page, and polls until the signed-in user approves. No key copy/paste is required. On a headless machine, add --no-browser and open the printed link elsewhere. The CLI exchanges approval for a computer-only key, verifies /remote-servers/preflight, stores it in a local 0600 config file, and never displays it.

The share command selects the reviewed environment, checks it, starts or reuses the exact loopback MCP tool set, runs the TU Platform preflight, and keeps the private relay in the foreground until Ctrl-C. Override defaults only when needed:

tu remote share scanvi --name my-scanvi-remote --workers 1

Use tu remote run scanvi for local-only operation. Sharing does not publish a tool or prove scientific accuracy.

In an interactive terminal, sharing automatically starts the same browser flow when the key is missing, expired, or revoked. A malformed or revoked explicit TOOLUNIVERSE_SERVICE_KEY fails fast instead of being silently replaced; unset or correct it, then run tu remote login. Non-interactive jobs also fail fast. Use tu remote logout to remove only the locally stored key.

Deploy#

pip install -r requirements.txt          # scvi-tools + scanpy
python scanvi_tool.py                       # starts the MCP server on 127.0.0.1:8027

Input is referenced by adata_path (a server-accessible .h5ad of raw UMI counts), since single-cell matrices are large. The AnnData must carry a labels_key obs column where some cells hold their known cell type and the unlabeled cells hold the unlabeled_category sentinel (default "Unknown"). Raw counts are preserved in a counts layer before training. Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse#

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