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Post-Installation Configuration of SQL Server Instance on EC2

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AWS Cloud Formation allows automated creation of EC2 instances in Windows Server Failover Cluster with SQL Server installed on top in Failover Cluster Instances. There is a lot of documentation about this and AWS themselves provide template to create clusters. However, I can't find any reference to automating the post-installation configuration. We need to make several changes to the default configuration such as setting up dbmail, changing the MAXDOP and adding backup jobs etc. The Powers That Be want instance creation to be as automated as possible but I've not been able to find any way to add these steps to the Cloud Formation templates. Is it actually possible to do this?

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