uabbds/ratlas repository overview

⁠Overview

The container contains dependencies needed to deploy the ratlas app to UAB's cloud.rc OpenStack infrastructure. The main public hosting location currently is: https://day-lab.shinyapps.io/ratlas/⁠ ; however for internal development, tests are performed in cloud.rc

⁠Running the app with Docker (for developers/maintainers only)

A Docker container has been created for the deployment of the app in UAB's cloud.rc. The pre-requirements to running the container is to ensure you have a copy of the latest code from the app (from https://github.com/Jeremy-Day-Lab/ratlas/⁠) and a copy of all the on-disk datasets hosted in Box (if you are not a member of our team, but would like a copy of the original R objects, please contact Dr. Jeremy Day. His contact information can be found at: https://day-lab.org/uab⁠

To make use of the container in your own computer (for local tests etc.), please see the following steps:

• git clone this app repository and cd to it from your computer

• Run the container with the following command (where pwd should be path upstream of the ratlas directory where app code is located. Thus, be sure to go to this cloned repository):

docker run -d --rm --user shiny -p 3838:3838 -v `pwd`/ratlas:/srv/shiny-server/ -v `pwd`/shiny_app_logs:/var/log/shiny-server uabbds/ratlas:latest

Open your browser, and go to local localhost:3838

Once finished don't forget to stop the container with

docker ps # find docker container id
docker stop <container_id>

⁠Running the app with Docker in cloud.rc

The above directions also apply to launching the app in cloud.rc. But please note that you should deploy the app with the use of the --restart always flag instead of --rm due to automatic server reboots:

sudo docker run -d --restart always --user shiny -p 3838:3838 -v `pwd`/ratlas:/srv/shiny-server/ -v `pwd`/shiny_app_logs:/var/log/shiny-server uabbds/ratlas:latest

⁠Citation to Ratlas

If this application benefits your work, we kindly ask to acknowledge the app by including the following DOI: