To run your javaCup, in the directory that is one layer above java_cup, type
java java_cup.Main < yourCupFile
The above command will generate the parser. It needs to work together with a scanner.
You can also look at the script files calc and calc2, to see the sequence of command to run the program. Note that JLex package should be also under your current directory. You can run those commands in sequence automatically.
In Unix/Linux/Ubunto/OS X, type
calc
to run the sequence of command. Before the first time you run it, you need to change the access mode by typing
chmod 755 calc
In Windows command line, you need to save the file as