Question

I am developing a dynamic app generator, so I would need to run the command on a runtime basis using Java on a server

Answer 1

From the Android Developer site:

Managing Projects from the Command Line

Building APK from Command Line

You will need Gradle to build from the command line. Once you have that you can create the APK like this:

Windows:

> gradlew.bat assembleRelease

Unix:

$ ./gradlew assembleRelease

This creates your Android application .apk file inside the project
bin/ directory, named -unsigned.apk.