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Can you re-try using the absolute path of jps in your if statement?

If you want to check that the process: cq5-author-4502.jar is running and do some action, then you can try:-

if [ `jps -l | grep cp| wc -l` -eq 0 ]
then
echo "Process is not running"
...

Is this what you are trying to do?

CMDPATH1="/usr/jdk/jdk1.5.0_24/bin"
CMDPATH2="/usr/jdk/instances/jdk1.5.0/bin"

if [ -d $CMDPATH1 ]
then
# $CMDPATH1/cmd - Execute your command
elif...