Using the Executable JAR file

The Executable JAR file is an all-in-one Java library that contains the Jalview application and all of the supporting libraries that are needed to make it run.

Since it is only a Java library file, you will need a Java JVM to run Jalview using the executable JAR.

If you need to install a JVM please see the Installing on Unix Java 8 Required section for suggestions.

You can run the JAR with

java -jar jalview-all-2.11.3.3-j1.8.jar

As JAR files should be already associated with the java binary often you might only need to double click on the JAR file in a file manager to open Jalview.

Drawbacks

Whilst this is probably the easiest way to run Jalview on an exotic platform, there are some drawbacks to using the Executable JAR:

File associations for, e.g., sequence files will not be set to link with Jalview.
The JAR does not use Jalview’s launcher application which also checks for updates.

Thanks to ej-technologies for granting a free install4j license to the Jalview Open Source Project. Jalview's desktop installers were built with the install4j multi-platform installer builder and Gradle.