Liu Bo and Ravi Madduri from the University of Chicago’s Computational Institute, under the guidance of Ian Foster, have increased the analysis capabilities available within the CVRG version of Galaxy. Based upon requirements gathered from members of the NHLBI-funded Progenitor Cell Biology Consortium, Bo and Ravi added the following RNA-Seq tools: Tophat, Cufflinks and its sister applications (cuffcompare, cuffmerge and cuffdiff), and cummeRbund. Following the deployment, Bo and Ravi integrated these tools into an analysis workflow, extending a workflow designed by Benjamin King at Mount Desert Island Biological Laboratory. The workflow gets data from a Globus Online endpoint and processes them with Tophat, Cufflinks and cummeRbund, resulting in a plot produced by cummeRbund. These tools and this workflow are available in the CVRG-Galaxy, running on Amazon EC2, under a research grant from Amazon. CVRG-Galaxy is available through the CVRG Portal.