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 fmschulz/omics-skills --skill tracking-taxonomy-updatesgit clone --depth 1 https://github.com/fmschulz/omics-skillsWrote 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/fmschulz/omics-skills/tracking-taxonomy-updates)<a href="https://agentmods.dev/skills/fmschulz/omics-skills/tracking-taxonomy-updates"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/tracking-taxonomy-updates.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00053 | $0.01207 |
| Opus 5 | $0.00026 | $0.00603 |
| Sonnet 5 | $0.00011 | $0.00241 |
| Haiku 4.5 | $0.00005 | $0.00121 |
Grade A, and why
tracking-taxonomy-updates 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 2d 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 — 107 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Tracking Taxonomy Updates
Use authoritative sources to report taxonomy changes with explicit versions, dates, and provenance.
Instructions
- Determine scope (domain, timeframe, output type).
- Pull authoritative updates and release notes.
- Extract versioned changes and impacts.
- If assigning taxonomy for any assembly, MAG, SAG, isolate genome, bin set, or contig FASTA, start with a QuickClade first-pass domain screen through the BBTools container. Save both per-input and
percontigresults before choosing downstream tools. - Route from the QuickClade domain screen:
- Bacteria or Archaea -> run GTDB-Tk for genome taxonomy. If the GTDB-Tk reference package is missing, set up/download it under the project/reference DB root, set
GTDBTK_DATA_PATH, and record the release before running classification. - Viral or virus-like -> route to
/bio-viromics; use vConTACT3 for phage/prokaryotic-virus gene-sharing taxonomy and GVClass for giant-virus/Nucleocytoviricota candidates. - Eukaryota -> run EukCC for eukaryotic MAG/genome QC and taxonomy context.
- Mixed, low-confidence, or conflicting domains -> split or flag contigs for manual review before domain-specific classification.
- Bacteria or Archaea -> run GTDB-Tk for genome taxonomy. If the GTDB-Tk reference package is missing, set up/download it under the project/reference DB root, set
- Normalize IDs and taxonomy strings across tools.
Convert QuickClade machine output with
scripts/quickclade_to_routing.pyso every downstream decision uses the documenteddomain_routing.tsvschema. - Deliver a versioned report with conflicts flagged.
- Submit GTDB-Tk, EukCC, vConTACT3, and GVClass work through
scripts/submit_taxonomy.sh; do not run these compute-heavy commands on a login node.
Quick Reference
| Task | Action |
|---|---|
| Sources | See reference/sources.md |
| Tools | See reference/tools.md |
| IDs/ranks | See reference/ranks-and-identifiers.md |
| Report template | See reference/report-template.md |
| QA checklist | See reference/qa-checklist.md |
| Release snapshots at authoring time | See reference/last-verified-snapshots.md (examples only — re-check sources for "latest") |
| Environment | Use the project's pinned Pixi environment and record its lockfile |
| Normalize QuickClade | uv run --script skills/tracking-taxonomy-updates/scripts/quickclade_to_routing.py quickclade.tsv --sample-id S1 --output domain_routing.tsv |
| Submit downstream classification | SLURM_ACCOUNT=... scripts/submit_taxonomy.sh gtdbtk bins results/taxonomy/gtdbtk |
What ships with it
10 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.
- fixtures/quickclade-machine.tsv 264 B
- reference/last-verified-snapshots.md 2.0 KB
- reference/qa-checklist.md 1.6 KB
- reference/ranks-and-identifiers.md 2.6 KB
- reference/report-template.md 2.0 KB
- reference/sources.md 4.4 KB
- reference/tools.md 9.7 KB
- scripts/quickclade_to_routing.py 4.0 KB runs code
- scripts/submit_taxonomy.sh 667 B runs code
- templates/taxonomy-tool.sbatch 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.
- 2d ago Changed d3190428b32a
- 8d ago First seen · 107 lines · 53 tokens per session scan A 183bffb5a686
tracking-taxonomy-updates is a skill published in the GitHub repository fmschulz/omics-skills (7 stars, last pushed 2d ago), licensed MIT. It adds 53 tokens to every session and 1,207 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 2026-08-31.
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