scVelo Remote Tool (MCP Server)#

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

scVelo dependencies, loopback discovery, and deterministic-mode execution passed on the upstream simulation with aligned finite pseudotime/confidence for 300 cells. 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.

  • Operation: run_scvelo_velocity

  • Start: python -m tooluniverse.remote.scvelo.scvelo_tool

  • Endpoint: http://127.0.0.1:8025/mcp

  • Provider configuration: set TOOLUNIVERSE_REMOTE_DATA_ROOT; approved H5AD inputs need scientifically suitable spliced/unspliced layers.

  • TOU check: tu doctor --forward http://127.0.0.1:8025/mcp --json

  • Private relay: tu serve --share --forward http://127.0.0.1:8025/mcp --name validation-scvelo --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 scvelo. 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 This implementation was imported as unpublished owner draft(s), configured with a 120-second timeout, and invoked through /expert-sessions/{id}/test.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 scVelo (RNA velocity; Bergen et al., Nature Biotechnology 2020) as a ToolUniverse remote tool: run_scvelo_velocity — infers RNA velocity from spliced/unspliced mRNA and returns a velocity-derived pseudotime ordering of cells plus a per-cell velocity confidence, and (with a cluster_key) the mean pseudotime per cluster as a coarse trajectory ordering.

Served remotely (not bundled) because scvelo pulls in scanpy + anndata + numba. The input .h5ad must carry spliced and unspliced count layers (e.g. from velocyto, kb-python / kallisto|bustools, or STARsolo); without them RNA velocity cannot be estimated and the tool returns a clear error.

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 scvelo

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 scvelo --name my-scvelo-remote --workers 1

Use tu remote run scvelo 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          # scvelo + scanpy + anndata
python scvelo_tool.py                      # starts the MCP server on 127.0.0.1:8025

Pipeline: scv.pp.filter_and_normalize -> scv.pp.moments -> scv.tl.velocity -> scv.tl.velocity_graph -> scv.tl.velocity_pseudotime + scv.tl.velocity_confidence.

Inputs are referenced by adata_path (a server-accessible .h5ad with spliced/unspliced layers), since single-cell matrices are large. Only bounded summaries (mean/min/max/std, per-cluster means) are returned; full per-cell arrays are included only for small datasets (n_cells <= 500). Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse#

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