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reynoldtan authored Feb 9, 2024
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# Setup and Configuration

***We are actively working to write documentation for this page as functionality is being developed. If you require more information on what to expect in this section, please feel free to [open a discussion on Github!](https://github.com/orgs/TripalCultivate/discussions)***
***We are actively working to write documentation for this page as functionality is being developed. If you require more information on what to expect in this section, please feel free to [open a discussion on Github!](https://github.com/orgs/TripalCultivate/discussions)***

**Configure Tripal Cultivate Phenotypes Module**

Getting to configuration menu:
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![image](https://github.com/TripalCultivate/docs/assets/15472253/72b499e1-d8cf-4025-9234-68b0e5d5fdcf)

With the appropriate permission, click on Tripal -> Extensions menu in the top main menu as shown in the screenshot above (marked No. 1). All Tripal 4 compatible modules will be listed in this page. Locate and click the link Tripal Cultivate Phenotypes Configuration (marked No. 2) to load a detailed listing of configuration pages available.

![image](https://github.com/TripalCultivate/docs/assets/15472253/2955244f-2e1d-4fe1-bbc5-416cbaf7a61b)

Configuration Menu Options
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1. **R TRANSFORMATION RULES**
Tripal Cultivate Phenotypes supports R language for statistical computing by providing syntactically valid version of trait or values. Use R Transformation Rules configuration page to define standard transformation rules to apply to trait or string when converting to R version.

3. **WATERMARK CHART**
Every diagram generated by Tripal Cultivate Phenotypes can be superimposed with personalized logo or text logo to ensure proper credit and indicate authenticity. Use Watermark Chart configuration to set watermarking scheme of modules.

4. **ONTOLOGY TERMS**
Tripal Cultivate Phenotypes require that phenotypic traits be housed in a Controlled Vocabulary (CV) and pre-define terms used throughout the various processes. Use Ontology Terms configuration to setup terms that best support your data.

Switch Configuration Pages
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Navigate from one configuration to another by using the top page tabs as shown in the screenshot below (marked No. 1).

![navigate config](https://github.com/TripalCultivate/docs/assets/15472253/e64ee0a6-afa6-4e64-a421-4de413bc91e9)



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