I have not tried autostart on Windows instances in EC2, but here is a support document on how to enable it.
We boot our Windows instances using custom AMI with the Windows installer already installed. The boot belt installer reads the URL from user data at startup. The URL points to a ZIP file stored in S3. The installer then downloads, unpacks, and executes the actual application installer — in our case, a simple CMD fie.
These settings allow us to have one basic AMI, and then be able to easily overlay 15+ different application configurations (without the need to restore AMI). If you have only one application configuration, this may be redundant for your situation.
The only problem we encountered was that our installation service started earlier - changing the service’s startup mode to “Automatic deferred” fixed this problem.
We wrote our installer for loading in Java, launched through YAJSW , because it is convenient for us. If you just need some simple Unix tools, most of them can be precompiled for Windows, for example wget .
For something completely different, you can try PsExec to configure the instance after loading it.
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