setup-boltz-remote-tool

name	setup-boltz-remote-tool
description	Set up, launch, validate, and troubleshoot the Boltz-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.

Set up Boltz-2 as a remote tool

Validation status (2026-08-16): Boltz 2.2.1 and the official checkpoints ran on the NVIDIA GB10 in one repaired direct MCP call and three authenticated Platform calls, each returning six finite affinity values in 63.6-66.5 seconds. The upstream MSA service timed out during validation, so those successful calls explicitly used bounded single-sequence mode. Missing, oversized, malformed, or non-finite affinity artifacts now fail closed. Public publication, cross-user isolation, broad concurrency, recovery, biological accuracy, and the live MSA path remain unvalidated; keep this deployment private.

Prerequisites

• Run from the ToolUniverse repository root on Linux with Python 3.12.3.
• CUDA GPU strongly recommended; CPU is not a practical production target.
• Keep provider data, weights, caches, and credentials outside Git.
• Bind to loopback. A non-loopback bind requires TOOLUNIVERSE_API_TOKEN; never put it in arguments or results.

Run the standard-library contract check before downloading large dependencies:

python scripts/remote_validation/setup_skill_preflight.py --implementation boltz

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

python3 -m venv .venvs/boltz
. .venvs/boltz/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .
python -m pip install fastmcp boltz

Package/network-dependent commands must be rerun in a clean environment before marking this skill complete.

Obtain credentials, data, and model weights

• Keep Boltz/model caches below caches/boltz. use_msa_server=true needs the upstream MSA service. Use false only when lower-quality single-sequence inference is acceptable. Review Boltz model/code and ligand-data licenses.

Authorize once, then share with one short command

After installing dependencies, exporting the provider resources above, and installing the pinned relay SDK described under Connect below, run from the repository root. Log in only 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 one short command:

tu remote share boltz

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 the 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 runs environment and TU Platform preflights, starts or reuses the exact loopback endpoint, validates discovery, and keeps the relay in the foreground until Ctrl-C. It automatically uses the reviewed Python, name, and worker count. Override them only when needed:

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

Use tu remote check boltz for a non-sharing readiness check and tu remote run boltz for a local-only foreground server.

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 local copy. Use tu remote logout --revoke to revoke the computer-only platform connection first; the server record remains offline for owner inspection.

Start and verify locally

mkdir -p caches/boltz runs/boltz
python -m tooluniverse.remote.boltz.boltz_mcp_server

The Streamable HTTP endpoint is http://127.0.0.1:8080/mcp. In a second activated shell run:

python - <<'PY'
import asyncio
from fastmcp import Client

async def main():
    async with Client("http://127.0.0.1:8080/mcp") as client:
        print([tool.name for tool in await client.list_tools()])

asyncio.run(main())
PY

Confirm discovery contains boltz2_docking; stop on empty, duplicate, or schema-drifted discovery.

Connect to ToolUniverse Connect

The tuplatform-connect relay is not yet published on PyPI. Install the reviewed public wheel below; its SHA-256 is pinned. Interactive sharing uses browser device authorization, so no key copy/paste or GitHub access is required.

python -m pip install fastmcp pyyaml "tuplatform-connect @ https://connect.aiscientist.tools/downloads/tuplatform_connect-0.3.0-py3-none-any.whl#sha256=3fad5eee5ecf7887a693d93ccd1aa112dc0955617a885d1fc3daded0030f9ae0"
tu doctor --forward http://127.0.0.1:8080/mcp --json
tu serve --share --forward http://127.0.0.1:8080/mcp --name validation-boltz --workers 1

Prefer browser device authorization. For CI or migration, supply TOOLUNIVERSE_SERVICE_KEY only through a protected environment or use tu remote login --manual-key; never put a key in shell arguments.

The authenticated 2026-08-16 Platform matrix found all 30 private owner relays online and all 41 operations discoverable. All imports remained unpublished owner drafts and were invoked through /expert-sessions/{id}/test. This implementation's draft(s) used a 120-second timeout and remote max concurrency 1.

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.

Run a verified example

Operation: boltz2_docking

{"sequence":"ACDEFGHIKLMNPQRSTVWY","ligands":[{"id":"L1","smiles":"CCO"}],"sampling_steps":20,"recycling_steps":1,"use_msa_server":false}

Invoke the example through the live local MCP endpoint:

python - <<'PY'
import asyncio
import json
from fastmcp import Client

async def main():
    arguments = json.loads('''{"sequence":"ACDEFGHIKLMNPQRSTVWY","ligands":[{"id":"L1","smiles":"CCO"}],"sampling_steps":20,"recycling_steps":1,"use_msa_server":false}''')
    async with Client("http://127.0.0.1:8080/mcp") as client:
        result = await client.call_tool("boltz2_docking", arguments)
        print(result)

asyncio.run(main())
PY

Expected success shape: msa_mode plus an affinity_prediction object containing finite values, and optionally a bounded CIF structure. If Boltz exits without the affinity artifact, treat the sanitized error as a failure rather than a partial success. Check scientific meaning, output bounds, invalid-input behavior, and absence of paths, secrets, and traces.

Tune GPU and concurrency

• Use one worker as a conservative, unmeasured default.
• Measure cold start, two warm calls, then parallel levels 1, 2, 4, 8, and only 16 if memory permits.
• Record successes/errors, p50/p95, peak RAM/VRAM, utilization, queueing, cancellation cleanup, and recovery.
• Increase workers only after single-flight initialization and sanitized recoverable OOM/timeout behavior are proven.

Troubleshoot and clean up

• Import/executable failure: reactivate the isolated environment and reinstall its requirements.
• Missing artifact: inspect provider-only environment variables and approved relative files; never accept arbitrary caller model paths.
• 401/403 on deliberate network binding: configure matching TOOLUNIVERSE_API_TOKEN bearer auth; prefer loopback plus relay.
• Stop server/relay with Ctrl-C. If installed, run tuplatform-service uninstall --name validation-boltz.
• Revoke temporary keys. After confirmation, remove only .venvs/boltz, caches/boltz, and runs/boltz; never use a broad recursive target.

Use only official upstream documentation linked by the implementation README; do not substitute third-party model mirrors.