Boltz Check Status Skill for Codex

Workflow

If boltz-api is missing from PATH, use boltz-cli-setup for install/update guidance before retrying.

If a command reports missing or expired authentication, use boltz-cli-setup to start boltz-api auth login --device-code before retrying; do not ask permission first.

If the agent host sandbox blocks boltz-api install/auth/API calls, use boltz-cli-setup to request the host sandbox bypass/escalation needed for user-wide CLI install, browser login, credential storage, temp files, or API access before retrying.

Use this skill to recover state across sessions and to inspect or download results for prior Boltz jobs. No payload authoring — this skill only calls list / retrieve / download-results / download-status.

Use four modes:

• Local progress: if the user knows the run name / run dir, prefer download-status before remote API calls.
• List recent jobs: enumerate all six resources, merge, and sort by created_at descending.
• Retrieve one job: use the job ID prefix when known; otherwise probe resources until one succeeds.
• Resume/download results: run download-results with the original run name when possible. Never run start again to resume.

ADME jobs use the prefix adme_pred_* and show up in Modes 1-2 (list / retrieve) like the others. ADME has no download-results/archive step, so Modes 3-4 don't apply — recover its scores by re-running retrieve (read output.molecules[]) or from the local run.json.

Read references/resume.md before recovering a dropped session, mapping job ID prefixes, or choosing a run name for download-results. Read references/api.md for per-resource list columns, retrieve fields, and result semantics.

Command Pattern

# Replace placeholders with concrete absolute paths before running.

# Local helper: inspect local checkpoint state without API calls.
boltz-api --format json download-status \
  --name "<run-name>" \
  --root-dir "/absolute/path/boltz-experiments"

# Mode 1: list recent jobs across all 6 resources.
# Note: the CLI emits one JSON object per record (streamed, no {data:[]} wrapper).
# --limit is per-page and the CLI auto-paginates, so cap each explicit command with head.
boltz-api predictions:structure-and-binding list --limit 20 --format jsonl | head -20
boltz-api predictions:adme list --limit 20 --format jsonl | head -20
boltz-api small-molecule:library-screen list --limit 20 --format jsonl | head -20
boltz-api small-molecule:design list --limit 20 --format jsonl | head -20
boltz-api protein:library-screen list --limit 20 --format jsonl | head -20
boltz-api protein:design list --limit 20 --format jsonl | head -20

# Mode 2: retrieve by ID. Pick the resource from the ID prefix in the workflow
# notes above. If the prefix is unknown, run these one at a time until one succeeds.
boltz-api predictions:structure-and-binding retrieve --id "<job-id>" --format json
boltz-api predictions:adme retrieve --id "<job-id>" --format json
boltz-api small-molecule:library-screen retrieve --id "<job-id>" --format json
boltz-api small-molecule:design retrieve --id "<job-id>" --format json
boltz-api protein:library-screen retrieve --id "<job-id>" --format json
boltz-api protein:design retrieve --id "<job-id>" --format json

# Mode 3: resume download. Use the agent runtime's managed long-running command mode.
boltz-api download-results \
  --id "<job-id>" --name "<run-name>" \
  --root-dir "/absolute/path/boltz-experiments" \
  --poll-interval-seconds 30

Always Do This

• If the user has a run name / slug or run dir and only wants local downloader state, prefer download-status before retrieve.
• Use an absolute output root and keep passing it through --root-dir. Do not cd into the run directory; that makes later relative paths point at the run directory instead of the user's workspace.
• On an unfamiliar job ID, run Mode 2 (retrieve) before Mode 3 (download) so you capture idempotency_key.
• Prefer the original run-name slug over the job ID as --name — it resumes into the existing dir with cursor.
• In permission-gated agents such as Claude Code, keep each Boltz call as a top-level command that starts with boltz-api. Prefer running the six list / retrieve commands explicitly over generating them from a shell loop; a fixed | head -20 cap is okay when listing to avoid runaway streamed output.
• Prefer the agent runtime's background/non-blocking command mode for download-results. In Codex specifically, keep download-results in the foreground and set the shell tool yield to 1000 ms; Codex will return a session_id if the command is still running. Do not append & or use nohup in Codex because the tool runner may clean up shell-backgrounded descendants before .boltz-run.json is fully written.
• After the background/session starts, do not manually wait on it or run ad hoc polling loops. In Codex app/desktop runtimes with same-thread heartbeat automation support, schedule a heartbeat that checks download-status periodically, posts only material status changes or terminal completion/failure, and stops once terminal. If the current host has no heartbeat automation support, do not claim an automatic next check; report the job ID, run name, output directory, and the command needed to check download-status.
• download-results now emits machine-readable JSONL progress on stderr by default. Add --progress-format text --verbose only when you explicitly want human-readable logs.
• Prefer download-status for local checkpoint state. In Codex hosts with heartbeat automation support, use it for automatic follow-up and poll the saved session with an empty write_stdin only for interactive, user-requested progress checks. Don't loop retrieve unless the user wants fresh remote status.
• If retrieve surfaces only {"code":"VALIDATION_ERROR","message":"Request validation failed"} with no details, that's expected for predictions:structure-and-binding failures — other endpoints include field paths.
• Never run start again on a failed or interrupted job. Fix the payload and submit with a new idempotency-key, or just resume with download-results.

Escape Hatch

• Python SDK reference (per-resource list / retrieve methods): <https://api.boltz.bio/docs/api/python>
• CLI flag names: boltz-api <resource> list --help, boltz-api <resource> retrieve --help, boltz-api download-results --help, boltz-api download-status --help

Outputs

• Local helper / Mode 1 / Mode 2 print structured data to stdout; present as a table.
• Mode 3 writes recovered artifacts under <output-root>/<run-name>/ — same layout as a fresh run. Read references/resume.md for resume behavior.