Slingshot Remote Tool (MCP Server)#

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

R 4.4.3/Slingshot 2.14.0, loopback discovery, and a deterministic call passed with two lineages and bounded aligned pseudotime for 240 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_slingshot_trajectory

  • Start: python -m tooluniverse.remote.slingshot.slingshot_tool

  • Endpoint: http://127.0.0.1:8030/mcp

  • Provider configuration: set TOOLUNIVERSE_REMOTE_DATA_ROOT and optionally RSCRIPT_BIN; required obs/obsm keys must exist in the approved H5AD input.

  • TOU check: tu doctor --forward http://127.0.0.1:8030/mcp --json

  • Private relay: tu serve --share --forward http://127.0.0.1:8030/mcp --name validation-slingshot --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 slingshot. 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 This implementation was imported as unpublished owner draft(s), configured with a 120-second timeout, and invoked through /expert-sessions/{id}/test.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 Slingshot (Street et al., BMC Genomics 2018) — single-cell lineage and pseudotime inference — as the ToolUniverse remote tool run_slingshot_trajectory.

Given a low-dimensional embedding and cluster labels, Slingshot builds a minimum spanning tree on the cluster centroids to order them into smooth lineages, fits simultaneous principal curves, and assigns each cell a pseudotime along every lineage it belongs to. It is robust for tree-shaped differentiation and a standard trajectory method.

Served remotely because the engine is R/Bioconductor (slingshot). The Python side reads the .h5ad with scanpy, extracts the chosen embedding (obsm) and cluster labels (obs), and hands them to the bundled slingshot_trajectory.R (CSV interchange — no zellkonverter/basilisk required).

Anchor directionality with start_cluster (the known root) and/or end_clusters (known terminal fates) when available — strongly recommended, since otherwise lineage orientation is arbitrary.

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 slingshot

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 slingshot --name my-slingshot-remote --workers 1

Use tu remote run slingshot 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            # scanpy + numpy (Python side)
Rscript -e 'BiocManager::install(c("slingshot","jsonlite"))'   # R side
python slingshot_tool.py                    # starts the MCP server on 127.0.0.1:8030

Rscript must be on PATH (or set RSCRIPT_BIN). Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse#

Tool definition: src/tooluniverse/data/remote_tools/slingshot_tools.json (type: RemoteTool).