Did you mean the executable fails to run , if invoked from any other directory? This is rather a bug on the executable. One potential reason could be the executable requires some shared libraires from the installed folder. You may check environment variable LD_LIBRARY_PATH
If you're using Ubuntu, you can put a shell script in one of these directories: /etc/cron.daily, /etc/cron.hourly, /etc/cron.monthly or /etc/cron.weekly.