Borrowing it
Nothing to install: this file belongs to 45ck/open-genome-agent. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/45ck/open-genome-agent/main/.agents/skills/setup-workstation/SKILL.mdgit clone --depth 1 https://github.com/45ck/open-genome-agentWrote 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/45ck/open-genome-agent/setup-workstation)<a href="https://agentmods.dev/skills/45ck/open-genome-agent/setup-workstation"><img src="https://agentmods.dev/badge/skills/45ck/open-genome-agent/setup-workstation.svg" alt="Measured on agentmods" height="20"></a>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 | $0.00029 | $0.00331 |
| Opus 5 | $0.00015 | $0.00166 |
| Sonnet 5 | $0.00006 | $0.00066 |
| Haiku 4.5 | $0.00003 | $0.00033 |
Grade A, and why
setup-workstation 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 6d 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.
What it actually says
Setup workstation
Prepare or validate a local genome-analysis workstation. Use before the first run on a machine or when toolchain drift is suspected.
When to use
- new clone or new machine
- tool versions changed
- permissions or hook behavior need validation
Do not use when
- routine analysis on an already validated machine
Expected outputs
workstation_report.jsontool_versions.json
Goal
Validate that the local machine is ready for safe, reproducible genome analysis.
Procedure
- Detect the OS, shell, Python version, and writable workspace.
- Check whether expected tools are present:
python3samtoolsbcftoolsvepplink2nextflow(optional in the MVP)
- Record versions and missing tools into a workstation report.
- Verify that
runs/exists and that raw genome paths are not inside.git/. - Confirm hook scripts are executable where relevant.
Output contract
Emit a compact machine-readable report and a plain-language summary. Missing tools should be reported explicitly instead of guessed around.
Escalate when
- required tools are missing
- the repo is not trusted
- permissions or sandbox settings are unexpectedly broad
References
See references/README.md for durable notes and scripts/ for deterministic helpers.
What ships with it
2 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.
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.
- 6d ago First seen · 54 lines · 29 tokens per session scan A f366d3d3c275
setup-workstation is a skill published in the GitHub repository 45ck/open-genome-agent (4 stars, last pushed 2mo ago), licensed MIT. It adds 29 tokens to every session and 331 once invoked, about $0.0001 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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