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You don't provide too much information here, so I'll have to speak in very general terms. Linux is not Unix, though it is Unix-like. As there are issues even when moving from Unix to Unix (Solaris-IBM, HP-UX-Solaris, etc…), do not expect a seamless migration, particularly if your applications are home-grown. If your applications are from a major ISV, there is a better-than-average chance that they have a supported Linux version. Try to enlist the services of the company directly, or better yet, an experienced consultant that has worked with migrations on the platforms that you are working with.
If this is not an option, take it slow. Make sure you have a suitable test environment in which to perform your Proof of Concept (POC) on. Install your software on that test environment and bring over the data using NFS or FTP. I don't know if you have a database or not, but if you do you'll have to re-create the database and also make sure that the versions of software you are using are compatible with whatever you are trying to integrate with.
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