To run a JAR file from the command line in ubuntu using the following command:

java -jar filename.jar

Otherwise it is also possible to enable double clicking to run jar files too by the following simple steps:

1. Find the .jar file in the File Browser (a.k.a Nautilus)
2. Right click the .jar file > Properties
3. Click on the “Open With” tab along the top
4. Change the bullet to be Sun Java 6 Runtime
5. Click Close and you’re done.

Now you should be able to just double click the file and it will run just like most other files!