CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
( http://compbio.mit.edu/cummeRbund/ )  


Prerequisites for installing cumme=Rbund:
The linux package: libxml2-dev
In ubuntu:   sudo apt-get install libxml2-dev

R package: ggplot2
   install.packages("ggplot2",dependencies = TRUE)

To install cummeRbund on your R server, follow the directions in:
( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
   source("http://bioconductor.org/biocLite.R")
   biocLite("cummeRbund")

This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an output that can be used directly in cummeRbund.