Vipin, 
Search works pretty well on the toolshed - I'd recommend a search for (eg) 'star' before writing yet another rnastar toolshed wrapper and dependency package? There's an installable fubar package_rnastar and an rnastar wrapper based on Jeremy's code mentioned below - but working AFAIK - at least it installs and works fine here and on the GVL.  



On Thu, Sep 12, 2013 at 1:49 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
STAR aligner 


Whether you use this code or not, I do have one request: please put the output in BAM rather than SAM format in order to save disk space.

Best,
J.