Hello Carlos, I think we have had reports of problems installing say the newest tophat tool on older Galaxy versions because it uses newer features the older Galaxy and tool shed install code doesn't know how to handle. I see the cummerbund wrapper is using some stuff added over the last 18 months (the discovered_datasets tag on an output). Is it possible you are using an older Galaxy and can update? Otherwise - it might be worth trying to uninstall and reinstall? It would also be good if you post the relevant parts of the Galaxy logs during the install (this is how we tracked down the tophat issues). -John On Wed, Mar 11, 2015 at 4:15 PM, Carlos Lijeron <clijeron@hunter.cuny.edu> wrote:

Everyone,

I’ve been encountering problems when installing particular tools in a local Galaxy instance. One such tool is Cummerbund as you can see in link below:

https://www.dropbox.com/s/bmg4qcci97ayq2k/Cloning%20State.JPG?dl=0

Would you have a suggestion on how to troubleshoot failed tool installations that do not give an output error message?

Thank you all !

Carlos.

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