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You can deploy the application as it is by copying it to Unix box.
When you create application with deployment template, it create .bat files for windows and .sh files for Unix in your <App_path>/control directory.
Things to consider are path separator you use in AppConfig.xml if you using any external libraries in forge and configuration file names as in Unix system same file name with different case is considered different file unlike Windows. For example Pipeline.epx and pipeline.epx are two different files in Unix.