I could only find information of using Netbeans to package a JavaFX app into .deb, but I couldn't find any info on how to do this with IntelliJ.
I am using Gradle as the build tool.
Could you guys share some insight?
Just as Olga pointed out, her advice helped me:
in Project Structure | Artifacts, add there JavaFX app, in JavaFX tab define "deb" native bundle and build artifacts with Build -> Build Artifacts