If you are using the Software Deployment module to deploy the software and execute the script then you have an option to Install the application as a different user using the RunAs option. If it is a Custom script configuration, by default the logged on user is considered.
However, if you have any specific requirement on the 'User's session', i would be happy to assist you further.
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Using the Run As option, it forces to specific a user account and the pwd, which would be difficult to handle because of security reason and number of PC to be handled.
Is there any option which would run the package under logged user's session? Leaving the Run As field blank, the package is then deployed with system account, so is there any specific parameter which does the same job with logged user's account without using the pwd?