virusvariantviewr-rshiny-application's Introduction

VirusVariantViewR-RShiny-Application

VirusVariantViewR RShiny application for viewing output from VirusVariantViewR Snakemake workflow.

Please visit the VirusVariantViewR application:

How to use:

Clone the VirusVariantViewR workflow to process your data.
Clone this repo to your local machine or wherever you wish to run the R Shiny application.

git clone --recurse-submodules https://github.com/RachelRodgers/VirusVariantViewR-RShiny-Application.git

Download the results/ directory generated by the VirusVariantViewR workflow to your local machine or wherever you wish to run the R Shiny application. The best location to store the results directory is directly inside the R Shiny app repo.
Edit the VirusVariantViewR-RShiny-Application_config.txt file to contain the path to the results/ directory. This path can be absolute or relative to the repository. Please do not include a trailing slash. Only the first line in the file will be read to determine the location of the results directory.
Double check the dataSet.txt file inside the results/ directory. It should include the name of each directory of data that you wish to visualize, one name per line. Note this file is appended to each time the Snakemake workflow runs, so may not contain all the datasets you wish to include in the application, or could include too many.
Open the VirusVariantViewR_app.Rproj in RStudio. If not installed, install the "shiny" package:

install.packages("shiny")

Open app.R and hit "Run" in the top of the source pane. Please note that the program will automatically attempt to install any missing but required R packages. It is possible R will need to reload during this process, and upon restarting will stop. Simply hit the "Run App" button again to re-start the process.

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