# Directory Structure Validation

> Use when after editing core R scripts in the Core-Match repository and before running LipidMatch-4.2 analysis, to verify that developer modifications have been correctly distributed across the Flow version (LipidMatch_Distribution) and Modular version (FluoroMatch_Modular) directory trees.

- Skill: `holobiomicslab/directory-structure-validation` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/directory-structure-validation`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/directory-structure-validation/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: CC-BY-4.0
- Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/holobiomicslab/directory-structure-validation

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# directory-structure-validation

> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->
## Summary

Validates that edited script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) are placed into the correct target directories within LipidMatch-4.2 distribution to ensure developer changes integrate properly into both Flow and Modular analysis versions.

## When to use

Apply this skill after editing core R scripts in the Core-Match repository and before running LipidMatch-4.2 analysis, to verify that developer modifications have been correctly distributed across the Flow version (LipidMatch_Distribution) and Modular version (FluoroMatch_Modular) directory trees.

## When NOT to use

- When using pre-compiled binary distributions where script files cannot be edited or replaced
- When script files are being downloaded directly from innovativeomics.com/software (use official binary distribution instead)
- When working with a cloned Core-Match repository alone without an installed LipidMatch-4.2 distribution

## Inputs

- edited R script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R)
- LipidMatch-4.2 distribution directory structure (downloaded from InnovativeOmics)
- README or methods specification file documenting target paths

## Outputs

- manifest file mapping source files to target paths (CSV or JSON format)
- validated directory tree or layout document
- confirmation that all script files are placed in correct locations

## How to apply

First, identify the four edited script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) from your source submission package. Next, create a manifest file (CSV or JSON) that maps each source file to its required target path(s): Modular.r must be placed in both `LipidMatch-4.2\Flow\LipidMatch_Distribution` and `LipidMatch-4.2\FluoroMatch_Modular` to replace existing code; genEIC.r, MS1Spectragen.r, and Stats.R must all be placed into `LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts`. Then, verify that each target directory exists within your downloaded LipidMatch-4.2 distribution (typically downloaded from innovativeomics.com/software). Finally, generate a directory tree or layout document showing the final file placement structure to confirm all files are in their specified locations before executing analysis workflows.

## Related tools

- **LipidMatch** (target software distribution into which edited scripts must be integrated) — https://github.com/InnovativeOmics/Core-Match
- **FluoroMatch** (alternative analysis version of LipidMatch requiring Modular.r placement for integration) — https://github.com/InnovativeOmics/Core-Match
- **R** (runtime environment for executing edited script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R))

## Evaluation signals

- All four script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) are present in their specified target directories
- Modular.r exists in both `LipidMatch-4.2\Flow\LipidMatch_Distribution` AND `LipidMatch-4.2\FluoroMatch_Modular` directories
- genEIC.r, MS1Spectragen.r, and Stats.R all exist in `LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts`
- Manifest file entries match actual file locations verified via directory listing or tree output
- No orphaned script files remain in intermediate or incorrect directories

## Limitations

- Validation assumes target directories already exist within the LipidMatch-4.2 distribution; missing parent directories will prevent proper file placement
- Windows and Unix path separators differ (backslash vs. forward slash); cross-platform deployment requires path normalization
- No changelog is available to document which versions of scripts are compatible with which LipidMatch-4.2 releases; version mismatches may cause runtime errors
- The skill validates structural placement only; it does not verify script syntax, dependencies, or functional correctness

## Evidence

- [readme] Modular.r must replace existing code in both directories: "put Modular.r into two directories (replace existing code): `LipidMatch-4.2\Flow\LipidMatch_Distribution` `LipidMatch-4.2\FluoroMatch_Modular`"
- [readme] Other edited scripts go into the Scripts subdirectory: "Place any edited script files (genEIC.r, MS1Spectragen.r, Stats.R) into: `LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts`"
- [readme] Developers edit scripts on GitHub and must integrate into downloaded distributions: "**Developers can edit the main algorithms here on github** as a team. Then the code needs to be integrated by placing the edited code in the correct directory from the downloaded distribution"
- [readme] Users download the distribution from the official website: "For LipidMatch, FluoroMatch, and PolyMatch **users should directly download from innovativeomics.com/software** for the latest stable release."
- [readme] Installation is prerequisite to integration: "Install FluoroMatch or LipidMatch from InnovativeOmics.com"