Hi I downloaded and extracted the .chain files for liftOver and edited the .loc file. After restarting Galaxy I have the option to convert my files to the respective coordinates but when running the job I get the same error for each.
"Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/tools/extract/liftOver_wrapper.py", line 81, in raise Exception, 'Exception caught attempting conversion: ' + str( e ) Exception: Exception caught attempting conversion" I also found this in the handler.log file: "galaxy.tools DEBUG 2012-12-20 11:37:09,902 Error opening galaxy.json file: [Errno 2] No such file or directory: '/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/000/98/galaxy.json' " Do you know how could this be sorted? Thanks in advance, Nikos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
