I am currently using Amazon Web Services EC2 Windows 2012 instance for my application. I want to migrate over to an EC2 Linux server. What's the best way do this? I have been unable to find sufficient resources on this topic. We are currently using Hibernate and Spring frameworks with MySQL and Apache Tomcat servers.
AWS EC2: Migrating from Windows to Linux Server
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First thing is realizing the main problem is not the server software and operating system but your application. You need to be sure that your application runs on Linux and you don't have any Windows dependent libraries.
Then you can create a Linux EC2 instance (Ubuntu, RedHat or any other distribution). Roughly the steps could be these: