Currently after every system restart we are running Fredhopper by starting deployment agent and then starting indexer.
is there any way to configure fredhopper as a service so that is should restart automatically whenever system restarts.
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There are no Windows services delivered with Fredhopper.
Fredhopper recommends using the Windows Task Scheduler to start the deployment agent. They have a page on their Learning Center to help you with that (requires login). That is what I typically do and have not have any issues with it.
There is no mention of the indexer or other processes, but presumably you can use the same mechanism -- but only once the deployment agent is up and running.