You have to give run.sh permission to run on the linux server. do this with: "chmod ug+x run.sh"
run.sh is used on linux machines and runOnWindows.bat is used for windows
To run on a windows machine, change run.sh to runOnWindows.bat in the build.properties file. You'll also need to change the path to java and the path to other files inside of runOnWindows.bat.
-Peter