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 HolobiomicsLab/asb-skill-collections --skill repository-cloning-and-dependency-verificationgit clone --depth 1 https://github.com/HolobiomicsLab/asb-skill-collectionsWrote 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/holobiomicslab/asb-skill-collections/repository-cloning-and-dependency-verification)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/repository-cloning-and-dependency-verification"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/repository-cloning-and-dependency-verification/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/repository-cloning-and-dependency-verification"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/repository-cloning-and-dependency-verification.svg" alt="Reviewed on agentmods" width="80" 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 Privilege Escalation · line 47 Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
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 | $0.00021 | $0.01675 |
| Opus 5 | $0.00010 | $0.00838 |
| Sonnet 5 | $0.00004 | $0.00335 |
| Haiku 4.5 | $0.00002 | $0.00168 |
Grade A, and why
repository-cloning-and-dependency-verification 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 5d 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 — 101 lines — stays where its author put it; the contents beside it link to each section on GitHub.
repository-cloning-and-dependency-verification
Summary
Clone a scientific software repository from GitHub and verify that all required executable dependencies (shell scripts, R scripts, external tools) are present and properly configured for end-to-end execution on representative input data. This skill ensures that published computational workflows are reproducible before committing to full-scale analysis.
When to use
You have identified a published computational tool (e.g., SEACR for CUT&RUN peak calling) available on GitHub and need to confirm that the source code is complete, executable scripts are present, required dependencies (R, Bedtools) are available in your environment, and the tool can process representative input files (e.g., CUT&RUN bedGraph files) to produce expected output (e.g., BED files of enriched regions) before running it on your experimental data.
When NOT to use
- The tool is already installed and functioning in your environment via package manager or containerized distribution — verification is redundant.
- You are working with only pre-computed results and have no need to re-execute the source workflow.
- The repository is private or restricted and you lack access credentials to clone it.
Inputs
- GitHub repository URL or clone path (e.g., FredHutch/SEACR)
- Representative input data file in tool-specified format (e.g., CUT&RUN bedGraph file omitting zero-signal regions)
- Tool README or documentation describing expected input format and required dependencies
Outputs
- Cloned local repository directory with all source code and scripts
- Verification report confirming presence and executable status of shell and R scripts
- Tool-generated output file(s) in documented format (e.g., BED file of enriched regions with columns: chr, start, end, total signal, max signal, max signal region)
How to apply
First, clone the target repository using git clone to obtain all source code and scripts. Second, inspect the cloned directory structure to verify that executable shell scripts (e.g., SEACR_1.3.sh) and R scripts are present and have executable permissions set. Third, confirm that all external dependencies listed in the README (e.g., R, Bedtools) are installed and available in your PATH. Fourth, prepare a minimal test input file conforming to the tool's documented input format (e.g., a small CUT&RUN bedGraph file that omits zero-signal regions). Fifth, execute the tool end-to-end using the prescribed invocation pattern (e.g., bash SEACR_1.3.sh target.bedgraph control.bedgraph norm stringent output). Finally, verify that the expected output file is produced, contains the documented output structure (e.g., BED format with chr, start, end, total signal, max signal, max signal region columns), and exhibits reasonable coordinate ranges and signal values.
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.
- 5d ago First seen · 101 lines · 21 tokens per session scan A 8e5572c2d24e
repository-cloning-and-dependency-verification is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed today), licensed Apache-2.0. It adds 21 tokens to every session and 1,675 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 2026-09-06.
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