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On Linux (end eventually on Windows, no idea for Mac), there is a way to package "java -jar blup.jar" command along with the jar itself into a single executable file, see http://superuser.com/questions/912955/how-to-make-a-java-jar-file-to-be-a-single-file-executable ####################### 1- Create a stub: MYSELF=`which "$0" 2>/dev/null` [ $? -gt 0 -a -f "$0" ] && MYSELF="./$0" exec java -jar $MYSELF "$@" exit $? 2- Concatenate the stub and the jar into a new executable: cat stub.sh Main.jar > main.sh 3- Make the new file executable: chmod +x main.sh ####################### This is a nice thing and we should add such an option and functionality to the FatJarPackageWizard.