R Shiny Example Web App

Learn to build and run an R Shiny application on DNAnexus.

Creating the Web Application

Inside the dxapp.json, you would add "httpsApp": {"ports":[443], "shared_access": "VIEW"} to tell the worker to expose this port.

A license is required to run HTTPS apps on the DNAnexus Platform. Contact DNAnexus Sales for more information.

R Shiny needs two scripts, server.R and ui.R, which should be under resources/home/dnanexus/my_app/. When a job starts based on this applet, the resources directory is copied onto the worker, and since the ~/ path on the worker is /home/dnanexus, that means you now have ~/my_app with those two scripts inside.

From the main applet script code.sh, we simply start shiny pointing to ~/my_app repo, serving its mini-application on port 443.

main() {
  R -e "shiny::runApp('~/my_app', host='0.0.0.0', port=443)"
}

Note that for all web apps, if everything is running smoothly and no errors are encountered (the ideal case), the line of code that starts the server will keep it running forever. The applet stops only when it is terminated. This also means that any lines of code after the server starts will not be executed.

Modifying This Example for Your Own Applet

To make your own applet with R Shiny, simply copy the source code from this example and modify server.R and ui.R inside resources/home/dnanexus/my_app.

How to Rebuild the Shiny Asset

View dxasset.json file

To build the asset, run the dx build_asset command and pass shiny-asset, i.e. the name of the directory holding dxasset.json:

dx build_asset shiny-asset

This will output a record ID record-xxxx that you can then put into the applet’s dxapp.json in place of the existing one:

"runSpec": {
    ...
    "assetDepends": [
    {
      "id": "record-xxxx
    }
  ]
    ...
}

Build the Applet

Now build and run the applet itself:

dx build -f r-shiny-web-app
dx run r-shiny-web-app

Once it spins up, you can go to that job’s designated URL based on its job ID, https://job-xxxx.dnanexus.cloud/, to see the result.

Source Code

Get the full source code on GitHub