I am interested in using Cufflinks 2.0 on our local instance of Galaxy but I am 
not sure if it is supported yet. We did Galaxy update in early October and we 
tried to install cufflinks V2.0 and it seems to run. I get the output files and 
they have the genes listed but 0.000 for all results (using files that worked 
on previous version).

The output file summaries contain the following:

Info: ERROR: Unable to read builds file: [Errno 2] No such file or directory: 
'/opt/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt'
ERROR: Unable to read builds file: [Errno 2] No such file or directory: 
'/opt/galaxy/galaxy-d

Is there a fix for this error or do we need to go back to the latest supported 
version of Cufflinks and if so which version?

Thanks
Chris Bidwell



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