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is there a third party tool or a way to automate installing windows updates on windows clusters with sql server high availability groups installed? right now we have a manual process of installing then failing over etc.

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There is not a tool that offers an out of box solution. However, there are many orchestration tools you can utilize to build your own automation solution. A few that come to mind are System Center Orchestrator or Ansible. Not to say those are the only tools, or the best tools. In the orchestration solutions you can build out a multi step playbook. Steps can include, checking if a replica is primary, pushing patches, failing replicas over, and rebooting servers. When or if each step executes could be tied to the outcome of the step before it.

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