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 agentmods add skills/holobiomicslab/asb-skill-collections/binary-path-detection-and-validationnpx skills add HolobiomicsLab/asb-skill-collections --skill binary-path-detection-and-validationgit 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/binary-path-detection-and-validation)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/binary-path-detection-and-validation"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/binary-path-detection-and-validation.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 | $0.00055 | $0.01817 |
| Opus 5 | $0.00028 | $0.00908 |
| Sonnet 5 | $0.00011 | $0.00363 |
| Haiku 4.5 | $0.00006 | $0.00182 |
Grade A, and why
binary-path-detection-and-validation 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.
How it starts
The opening of the file, as written. The whole thing — 108 lines — stays where its author put it; the contents beside it link to each section on GitHub.
binary-path-detection-and-validation
Summary
A configuration-driven mechanism for detecting and validating required binary tool installations (bowtie2, samtools, R, Python) by querying the system PATH and version constraints, then generating an environment-specific locked configuration file. This skill ensures reproducibility by recording exact tool locations and validating minimum version requirements before pipeline execution.
When to use
When setting up a bioinformatics pipeline (particularly Hi-C data processing) that depends on multiple external binaries with version constraints, and you need to configure the environment in a way that is both portable across systems and reproducible across runs. Specifically: (1) users provide a configuration template with optional explicit paths, (2) missing paths must be auto-detected from $PATH, (3) detected tools must meet minimum version thresholds (e.g., samtools ≥1.9, Python >3.7), and (4) the final configuration must be locked to prevent accidental runtime modification.
When NOT to use
- When all tool paths are already hardcoded in pipeline scripts or environment modules—this skill is unnecessary if binaries are already resolved.
- If the pipeline does not have version constraints or does not require specific binaries—the overhead of path detection and validation adds complexity without benefit.
- When deploying via containerized images (Docker, Singularity) where dependencies are pre-installed and environment is fixed—detection is redundant in a sealed container.
Inputs
- config-install.txt template file (plaintext with placeholder entries for tool paths and cluster scheduler)
- System environment variables ($PATH)
- User-specified tool paths (optional, in config-install.txt)
Outputs
- config-system.txt (read-only locked configuration file with resolved paths for all dependencies)
- Installed or verified binary tools (bowtie2, samtools, R, Python) at specified locations
- Installation logs and version validation records
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 · 108 lines · 55 tokens per session scan A 43b34fa2eb5b
binary-path-detection-and-validation is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed yesterday), licensed Apache-2.0. It adds 55 tokens to every session and 1,817 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 2026-08-30.
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