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I am using Sitecore Azure Toolkit for packaging and deployment.

I was wondering if there is a way to add custom databases (databases created by myself, other than core, master, web, etc.) to the packages.

Or if there is a way to automatically (using Azure Powershell scripts) add the custom databases.

Thanks...

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A custom db really has nothing to do with Sitecore. You can either add it to the ARM template deployment like shown here: https://docs.microsoft.com/en-us/azure/templates/microsoft.sql/servers/databases

Or via powershell here: https://docs.microsoft.com/en-us/azure/sql-database/sql-database-get-started-powershell

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Does the custom db belong to the Sitecore environment? I.e. if it doesn't exist your custom application won't run? If this is the case, look at bundling the database as a custom module.

Documentation for creating a custom module: https://doc.sitecore.net/cloud/working_with_sitecore_azure_toolkit/packaging/the_web_deploy_packages_for_a_module

You could then also add into the module the XDT to update the connection strings as well as generating the database so that the Sitecore environment is updated post database creation.

A great example of adding connection strings would be the Sitecore 8.2 EXM packages where we had to add connection strings for EXM: https://dev.sitecore.net/Downloads/Email_Experience_Manager/35/Email_Experience_Manager_35_Update2.aspx

You could then create your own module installer JSON like the EXM one: https://github.com/Sitecore/Sitecore-Azure-Quickstart-Templates/tree/master/EXM%203.5.0/xp0

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