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I just came across an article regarding submitting app to Ubuntu Software Center

http://developer.ubuntu.com/publish/apps/other-forms-of-submitting-apps/commercial-software-faqs/

I'm currently maintaining a open source stock market software. I would say around 80% are Windows users, although the software itself can be executed in Linux too.

I would like to increase adoption of Linux users. Hence, distributing the software in most popular Linux distro will definitely help.

I was wondering, whether a pure Java written software will be accepted in Ubuntu Software Center? It requires JRE6 and above.

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Yep, there's no reason why not. Your package will just depend on JRE, so when installing your software, the USC will automatically install Java as well should it be missing.