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I am trying to log the applications that a user opens/closes. Is there a way to execute a script (Java,Python,etc) everytime an application (like firefox) is opened and closed?

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You can use a wrapper, e.g. possibly called firefox, which can be found earlier in your $PATH. For instance:

#!/bin/sh
[commands executed before Firefox starts]
/usr/bin/firefox "$@"
[commands executed after Firefox quits]

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