barqueShinyApp

A containerized Shiny app interface for BARQUE, the reproducible eDNA analysis pipeline.

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🐳 Why Run in a Container?

This application is designed to run inside a Docker container that includes all dependencies required by BARQUE, including:

• FLASH (v2.2.00)
• VSEARCH (v2.30.0)
• GNU Parallel
• etc.

See the BARQUE's documentation for the full list of dependencies.

Here is the full list of R, Python, and system dependencies included in the Docker image:

• R packages: shiny, shinydashboard, DT, dplyr, readr, remotes, pkgload, config, golem, shinyWidgets, bslib, reactable, cli, fontawesome, rsconnect, usethis, desc, httpuv
• Python 3 + packages: biopython, pandas, numpy
• System libraries: libcurl4-openssl-dev, libssl-dev, libxml2-dev, libgit2-dev, libglpk-dev, libharfbuzz-dev, libfribidi-dev, openjdk-11-jre-headless, build-essential, etc.

This approach ensures:

• 💡 Reproducibility: every user runs the exact same environment.
• 💻 Simplicity: no R, Python, or system-level installations are needed locally.
• 🔒 Isolation: the host system stays clean and untouched.

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🚀 Running the App in Docker

To build and run the app inside Docker:

git clone --recurse-submodules https://github.com/taq-community/barqueShinyApp.git
cd barqueShinyApp
docker build -t barque-app:dev .
docker run -p 3838:3838 -v $(pwd):/srv/shiny-server -t barque-app:dev

Run the app inside the container:

Then access the app in your browser at:

http://localhost:3838

This launches the full BARQUE environment with all the eDNA toolchain pre-installed.

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💻 Development (Optional - Local R Session)

If you want to develop or debug locally instead:

# inside R
golem::document_and_reload()
barqueShinyApp::run_app()

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🧪 Test Results

This project uses:

• devtools::check() for validation
• covr + covrpage for test coverage
• testthat for unit testing

See dev/ for development scripts.

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📬 Maintainer

Steve Vissault — steve.vissault@inrs.ca
Developed for the TAQ initiative on environmental DNA in Québec.