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 system-path-configuration-and-environment-setupgit 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/system-path-configuration-and-environment-setup)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/system-path-configuration-and-environment-setup"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/system-path-configuration-and-environment-setup/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/system-path-configuration-and-environment-setup"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/system-path-configuration-and-environment-setup.svg" alt="Reviewed on agentmods" width="80" 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 | $0.00045 | $0.01627 |
| Opus 5 | $0.00023 | $0.00813 |
| Sonnet 5 | $0.00009 | $0.00325 |
| Haiku 4.5 | $0.00005 | $0.00163 |
Grade A, and why
system-path-configuration-and-environment-setup 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 — 106 lines — stays where its author put it; the contents beside it link to each section on GitHub.
system-path-configuration-and-environment-setup
Summary
Configures tool dependencies and environment paths for a bioinformatics pipeline by editing configuration files and running automated dependency detection. This skill ensures that required tools (e.g., samtools, bowtie2) are correctly located and validated before pipeline execution.
When to use
You are setting up HiC-Pro or a similar multi-tool pipeline for the first time, or you need to validate that all required dependencies are installed and discoverable. Use this skill when the pipeline's installation documentation directs you to configure tool paths and verify dependency availability before running data processing workflows.
When NOT to use
- Your pipeline dependencies are already installed and working correctly, and you do not need to reconfigure or validate paths.
- You are running the pipeline via Docker or Singularity container, where dependencies are pre-configured and PATH setup is handled by the container environment.
- You are executing a single module or step that does not depend on the full dependency chain (e.g., a standalone R or Python script with self-contained imports).
Inputs
- config-install.txt (configuration template file with optional tool path entries)
- System PATH environment variable (for automatic tool discovery)
- Makefile and associated build system files
Outputs
- config-system.txt (resolved configuration file with validated tool paths)
- Tool installation logs (if automatic installation was triggered)
- Confirmed availability of samtools (>=1.9), bowtie2, R, Python (>3.7), and other pipeline dependencies
How to apply
Edit the config-install.txt file to specify the full path to each required tool binary (e.g., samtools >=1.9, bowtie2), or leave entries unset to allow automatic detection via the system PATH using the 'which' command. Then execute 'make CONFIG_SYS=config-install.txt install' to trigger dependency checking and configuration. The build system will validate tool availability, attempt to install missing dependencies if needed, and generate a resolved config-system.txt file containing all tool paths. Verify that all required tools are detected and recorded in the generated config-system.txt file before proceeding to pipeline execution.
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 · 106 lines · 45 tokens per session scan A 16d54d7cc3d8
system-path-configuration-and-environment-setup is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 2d ago), licensed Apache-2.0. It adds 45 tokens to every session and 1,627 once invoked, about $0.0002 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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