Use something like:
REM Test for lock file
IF EXIST lock.txt (
REM Do nothing
) ELSE (
REM Create lock file
ECHO > lock.txt
REM Call your applications here
REM Delete the lock file afterwards
Since you've already written a batch file, I'll assume you're capable of integrating this into yours.
If you want to enhance it then you should write the process ID to the
lock.txt file and, if it exists, test if the process number in the file also exists before assuming that it's running. That way if the process dies and the lock file isn't removed, you won't get it incorrectly thinking it's still running the next time the batch file is run.