Hello, There are many ways to use Galaxy, and the tools offered/available in each is often a choice made by the group hosting the instance (not the version of the underlying code base): http://wiki.galaxyproject.org/Big%20Picture/Choices Wrappers for this tool are available from the tool shed: http://toolshed.g2.bx.psu.edu/ This tool and any of the others in the tool shed are intended to run in the latest Galaxy distribution. To get started with a local or cloud instance, please see: http://getgalaxy.org Tools are often submitted by public contributors as donated work to the community, so if you run into problems, the first place to start is to contact the repository authors. The repository will note contact information. And you are correct, the public Main Galaxy instance (http://main.g2.bx.psu.edu, aka "usegalaxy.org") does not host this tool, but the version of Galaxy is not a factor. Some tools are hosted on the public site and others are better suited for local/cloud use due to resource or other reasons. There are also other public Galaxy instances that may be of interest to you. These can be explored to see if the tools or services offered fit your needs. This wiki lists the sites known to us: http://wiki.galaxyproject.org/PublicGalaxyServers Concerning Cuffdiff - the public server has been very busy. If your jobs are in a grey "waiting to run" state, the best strategy is to leave these alone until they process. If any have ended in what appears to be a cluster failure (this can occur occasionally during peak usage times), then at least one re-run is recommended, and if problems continue that you cannot diagnose, please submit a bug report and we can provide some feedback (leaving all inputs/outputs undeleted). While queuing jobs, it is important to not delete and then restart them, as this effectively moves them back to the end of the processing queue. If you jobs are urgent, then a local or cloud instance is recommended. Hopefully this helps to clarify how the tools work! Take care, Jen Galaxy team On 1/29/13 2:55 PM, Ben Ben wrote:

Hi All,

Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differentially expressed transcripts from read alignments)? Any alternative?

As far as I know, *Penn State Version* doesn't integrate the DESeq function.*And Cuffdiff seems stop working in Penn State *

Thanks very much for the response!!

Best wishes,

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