Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add TianGzlab/OmicsClaw --skill orchestratorgit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/tiangzlab/omicsclaw/orchestrator)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/orchestrator"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/orchestrator.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Rogue Agent · line 3 Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00060 | $0.01232 |
| Opus 5 | $0.00030 | $0.00616 |
| Sonnet 5 | $0.00012 | $0.00246 |
| Haiku 4.5 | $0.00006 | $0.00123 |
Grade A, and why
orchestrator scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 93 lines — stays where its author put it; the contents beside it link to each section on GitHub.
orchestrator
When to use
The user asks a natural-language omics question (e.g. "find spatial
domains in my Visium data", "call CNVs from this BAM", "run DE on
my proteomics CSV") and you need to dispatch to the correct skill
across the 6 routed OmicsClaw domains (_DOMAINS at omics_orchestrator.py:190). Three routing modes:
keyword(default) — fast lexical match againsttrigger_keywordsin every skill'sskill.yaml.llm— LLM-based query → skill match (slower, more flexible).hybrid— keyword first, LLM fallback when ambiguous.
If the target skill is already known, invoke it directly — this
skill exists to dispatch ambiguous queries, not as a wrapper.
For scaffolding NEW skills use omics-skill-builder.
Inputs & Outputs
Outputs
result.jsondemo_report.txt- Produces artifact
orchestrator.route_decisionasresult.json(json)
Flow
- Parse
--query(or--demo). - If
--inputis provided, calldetect_domain_from_path(omicsclaw.loaders) to bias domain selection. - Dispatch to
route_keyword/route_query_unifiedper--routing-mode(omics_orchestrator.py:24-26imports). - Resolve the chosen skill via
resolve_capability(omicsclaw.core.capability_resolver); look up registry entry viaomicsclaw.core.registry.registry. - Write
result.json(omics_orchestrator.py:409); print the selected skill name + suggested CLI invocation.
Gotchas
--queryREQUIRED unless--demo. No explicit raise — argparse accepts aNonequery, the run still exits 0 and writesresult.jsonwithdetected_skill: null,coverage: "no_skill". Always pass--queryfor real use.--routing-modeis IGNORED when--queryis set.omics_orchestrator.py:374-389dispatches--queryruns toresolve_capability(capability-resolver — keyword-based with no mode parameter).--routing-modeonly takes effect for file-only routing (:393route_query_with_mode) and--demo(:362run_demo). For LLM-routed queries, call the unified router directly.- Missing
LLM_API_KEYSILENTLY falls back to keyword routing — no error.omicsclaw/routing/llm_router.py:48-50logs a warning and returns(None, 0.0); the orchestrator continues with keyword/capability routing. The run still exits 0 — inspect logs to confirm which mode actually fired. keywordmode depends ontrigger_keywordsinskill.yaml. Stale or missing keywords degrade routing quality silently. The 95 v2 skills' keyword tables are loaded on every call via the registry.- No analysis is performed. This skill only emits a routing decision in
result.json; it does NOT execute the chosen downstream skill. The user (or a wrapping orchestration script) must invoke it. - Demo and real-query outputs are mutually exclusive.
--demowrites ONLYoutput_dir/demo_report.txtand returns atomics_orchestrator.py:363; real--query/--inputruns write ONLYoutput_dir/result.json(:409). The two never co-exist in the same run.
What ships with it
12 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- INDEX.md 1.2 KB
- omics_orchestrator.py 16 KB runs code
- omics-skill-builder/omics_skill_builder.py 7.4 KB runs code
- omics-skill-builder/references/methodology.md 3.2 KB
- omics-skill-builder/references/output_contract.md 1.8 KB
- omics-skill-builder/references/parameters.md 473 B
- omics-skill-builder/SKILL.md 4.9 KB
- omics-skill-builder/skill.yaml 1.2 KB
- references/methodology.md 11 KB
- references/output_contract.md 1.6 KB
- references/parameters.md 281 B
- skill.yaml 1.0 KB
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago First seen · 93 lines · 60 tokens per session scan A 1f9f51afe799
orchestrator is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 60 tokens to every session and 1,232 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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