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I'm looking into using group policy to deploy a couple of applications. I want to have the log of each installation written to a shared folder on a file server for tracking purposes.

I can create the log if I pass the appropriate parameters. For example: msiexec /i Package.msi /l*vx c:\Package.log

However using group policy for the deployment, you can't pass any parameters to the installation file.

Is there anyway to specify the log file location in the process of creating the msi package?

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You should create an MST file to go with your MSI, that would include the options that you need. You can then deploy it through AD.

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