RseqFlow is an RNA-Seq analysis pipeline, which offers an express implementation of analysis steps. It can perform pre and post mapping quality control (QC) for sequencing data, calculate expression levels for uniquely mapped reads, identify differentially expressed genes, and convert file formats for ease of visualization. RseqFlow offers two run mode options. One is a workflow mode which uses Pegasus to manage the entire run process, the other is a unix shell run mode which allows users to execute each branch of analysis from the command line.
The description of the pipeline and instructions for running it can be found on google code.