Hello Nikolay, There are two version numbers associated with tools - the wrapper version and the underlying tool/binary version. For Cuffdiff, the binary on the pubilc Galaxy server is at 2.1.1, and this can be seen in a dataset's result "info" field once a job is complete. (The wrapper is 0.0.5). Hopefully this helps to explain, Jen Galaxy team On 5/24/13 9:23 AM, Nikolay N. wrote:

Hi,

I noticed that the version of cuffdiff used in main.g2.bx.psu.edu <http://main.g2.bx.psu.edu> is really obsolete (0.0.5) whereas the most recent version is 2.1.1.

Is there a chance that a more up-to-date version will be ever installed on the main galaxy instance?

many thanks, Nikolay

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