Project organization

Project organization

All project repositories used in this course are pre-installed in your environment.

📁 Where to find them

Projects are located in:

cd ~/GitHubRepos

To view the full list of repositories (including dev and stable subfolders), you can run the following in the Terminal:

find ~/GitHubRepos -maxdepth 2 -exec ls -ld {} \;

This will show the folder structure and help you identify which projects are available.

🗂 ️Types of repositories

• Some repositories include only a dev version → they are currently under development.
• Others include both:
  • stable/: the latest release from the main branch.
  • dev/: the most recent push to the dev branch.

📦 List of projects

Repository	Versions	Description	Main Script	GitHub
geoflow-tunaatlas	stable + dev	Prepares the Global Tuna Atlas datasets (Levels 0, 1, 2; effort and CPUE) and deploys them to Zenodo. Also contains Dockerfiles for downloading source datasets and running workflows.	launching_jsons_creating_GTA.R	GitHub
tunaatlas_pie_map_shiny	stable + dev	A Shiny app for visualizing any dataset in CWP format with various plots and maps.	global.R	GitHub
shiny_compare_tunaatlas_datasets	dev only	A Shiny app to compare GTA datasets from zenodo DOIs.	global.R	GitHub
darwin_core_viewer	dev only	A basic Shiny app to visualize biodiversity data using the Darwin Core data format. Provides maps and plots. Designed as a starting point for custom apps.	app.R	GitHub

📌 Documentation for each project is available in the README.md files within the folders, and on the respective GitHub repositories.

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You can open and explore any of these projects directly in RStudio by navigating to the appropriate folder using the Files tab, or via setwd("~/GitHubRepos/<project>/<version>/<project>") in your console.

Ready to run your first workflow? Jump to the next section Running Rscripts in a loaded project about the running of some scripts in the Vlab infrastructure of BlueCloud 2026.