Did the Tuxedo suite not work out for you in the end? Or the other
that Ross suggested? These are both pipelines that are in common use.
Using a cloud Galaxy and installing tools from the Tool Shed is
for certain tools, perhaps that is the problem? Many tools now have
automatic dependency installation, making set-up much easier. For a
demonstration, watch the Channel: Galaxy ToolShed videos at Vimeo:
You also may want to look at some of the miRNA specific tools in the
Tool Shed. They can be found under "Sequence Analysis". Most of these
have online documentation, or the tool author includes documentation,
that you can review to see if the tool is a good fit for what you want
to do (if it is not expression analysis anymore, or you want to try
something different like DESeq).
Hopefully this helps,