GMM Deployment
This guide outlines the steps to access and set up the GMM application using RStudio on OnDemand. This following steps are:
- Login to OnDemand
- Open RStudio and Install Dependencies
- Clone Code Repository and Download Dependencies
- Configure and Launch ShinyApp
First, navigate to the OnDemand login page and enter your credentials to log in.
From the OnDemand dashboard, select the latest version of RStudio.
Configure RStudio with the default settings, ensuring that the R version is set to 4.2.3. For runtime hours, CPUs, and Memory configuration, set these to 1 as we only need RStudio to install dependencies.
Click the Launch button to start RStudio.
Once RStudio is ready, click on Connect to RStudio Server. A new browser tab will open.
Select the Terminal in RStudio and enter the following command to clone the repository:
git clone https://github.com/WEHI-ResearchComputing/Genomics-Metadata-Multiplexing.git gmmYou should now see a gmm folder in the file browser.
Navigate to the gmm folder and pull the ShinyServer content:
cd gmm
git pull origin shinyServerSet this folder as the working directory.
Open setup.R and run the script to install the required R dependencies.
You can click the source button or use the command line:
source("~/gmm/setup.R")Navigate to the Shiny App configuration section.
Configure the Shiny App with the following settings:
- Partition: interactive
- R Version:
4.2.3 - #CPU:
4 - Memory:
8GB - Runtime hours:
24 - Shiny App directory: Select the
gmmfolder
Click launch and wait for the app to start. Once launched, you will see the following page:
Finally, click Connect to Shiny App to access the application.
This documentation has been updated for clarity and thoroughness, ensuring users can follow the steps to set up and launch the Genomics Metadata Multiplexing project successfully.