Version specific deployment configuration

version-specific-deployment-configuration

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Summary

Configure and deploy edited R scripts into version-specific directories within the LipidMatch-4.2 distribution framework, ensuring correct parameter settings and file placement for either Flow or Modular analysis modes. This skill bridges developer-side algorithm edits on GitHub with end-user installations.

When to use

You have edited core R scripts (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) in the InnovativeOmics/Core-Match repository on GitHub and need to integrate those changes into a local LipidMatch-4.2 or FluoroMatch distribution. Use this skill when you must decide whether to target the Flow version (FLOW <- TRUE) or Modular version (FLOW <- FALSE), and route files to the correct subdirectories to avoid conflicts between pipeline modes.

When NOT to use

• You are an end user downloading LipidMatch from innovativeomics.com for the first time — use the pre-packaged distribution directly without editing or redeploying scripts.
• Your edits are isolated to a single analysis and you do not need to integrate them into the main distribution framework for repeated use.
• You are uncertain whether Modular.r should replace existing code in both directories or only one — clarify with the development team before deploying.

Inputs

• Edited R script files (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) from InnovativeOmics/Core-Match GitHub repository
• LipidMatch-4.2 distribution directory tree downloaded from innovativeomics.com
• README or methods specification documenting target paths
• Information about intended analysis mode (Flow vs. Modular) and application type (Lipid, PFAS, or TWeen_pos)

Outputs

• Configured Modular.r with FLOW parameter set to TRUE or FALSE
• Deployed script files in correct version-specific directories (Flow and/or Modular paths)
• Manifest or layout document mapping source files to target paths
• Validated directory structure with all edited scripts in place and ready for execution

How to apply

After downloading the LipidMatch-4.2 distribution from innovativeomics.com, identify which pipeline mode (Flow or Modular) your edits target. For Modular.r, place the edited file into both LipidMatch-4.2\Flow\LipidMatch_Distribution and LipidMatch-4.2\FluoroMatch_Modular, replacing existing code in each. For all other edited script files (genEIC.r, MS1Spectragen.r, Stats.R), route them into the shared library path LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts. Open the main Modular.r file and set FLOW <- FALSE for Modular version or FLOW <- TRUE for Flow version. Additionally, toggle application-specific parameters: set Lipid <- TRUE and TWeen_pos <- FALSE for lipid analysis, or leave both FALSE to default to PFAS analysis. Verify all target directories exist; if they do not, refer to the distribution template or contact the developers.

Related tools

• LipidMatch (Target software framework into which edited scripts are deployed; supports both Flow and Modular pipeline modes) — https://github.com/InnovativeOmics/Core-Match
• FluoroMatch (Alternative LipidMatch-based distribution that shares the Modular.r script in FluoroMatch_Modular directory) — https://github.com/InnovativeOmics/Core-Match
• R (Execution environment for all deployed script files and configuration parameters)

Evaluation signals

• Modular.r file exists and contains the correct FLOW parameter value (TRUE or FALSE) matching the target pipeline mode
• All edited script files (genEIC.r, MS1Spectragen.r, Stats.R) are present in LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts
• Modular.r is deployed in both LipidMatch-4.2\Flow\LipidMatch_Distribution and LipidMatch-4.2\FluoroMatch_Modular directories if targeting Modular mode
• Application-specific parameters (Lipid, TWeen_pos) are set correctly in Modular.r and match the intended analysis type
• Directory manifest or layout document reconciles all source files to their target paths with no missing or conflicting mappings

Limitations

• Modular.r must be placed into two separate directories to support both Flow and Modular versions; failure to do so will break one of the pipeline modes.
• No changelog is provided in the repository, so developers must manually track which scripts were edited and communicate changes to the team.
• Configuration is file-path and parameter-based; no automated deployment or validation tool is mentioned, so manual verification is required.
• Edits made on GitHub are not automatically integrated into user distributions; developers must follow the manual deployment process and contact the team with major changes.

Evidence

• [readme] Install FluoroMatch or LipidMatch from InnovativeOmics.com: "Install FluoroMatch or LipidMatch from InnovativeOmics.com"
• [readme] Modular.r must be placed in two directories (Flow and Modular): "put Modular.r into two directories (replace existing code): LipidMatch-4.2\Flow\LipidMatch_Distribution LipidMatch-4.2\FluoroMatch_Modular"
• [readme] Other edited scripts are placed in the LipidMatch_Libraries/Scripts subdirectory: "Place any edited script files (genEIC.r, MS1Spectragen.r, Stats.R) into: LipidMatch-4.2\Flow\LipidMatch_Distribution\LipidMatch_Libraries\Scripts"
• [readme] FLOW parameter distinguishes Modular from Flow version: "For the Modular version set FLOW <- FALSE ... For the Flow version set FLOW <- TRUE"
• [readme] Application-specific parameters control analysis mode: "Make sure to toggle the following parameters depending on your application, if both are FALSE it defaults to PFAS analysis: Lipid <- TRUE TWeen_pos <- FALSE"
• [readme] Developers edit on GitHub and integrate into local installations: "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"