RSeqMule

It is a small tool chain that automatically downloads all necessary files include sources and annotations, and then compiles them for users. You can set up most of RNA Seq analysis tools and their dependencies with it and also can run analysis by tools of your choice. RSeqMule can generate the analysis scripts for later purpose, too.
Originally, it was designed to aid researchers to test various combination of tools for their RNA Seq analysis. Since there are quite a many RNA Seq tools which are newly announced and are based on the various platform, it is hard to test multiple tools without dedicated server manager especially most of them require their own unique dependencies.

It is still on its alpha status, though, I expect it will be officially launched at early 2014 as a beta version when the initial tests are completed. Currently, only preparation (download and compile) step and and script generation step are implemented for testing.

Program Sourceforge 
Manual  Download

Screenshots

First run (Software compile and installation step)

Analysis run

Generated batch script