I have recently migrated to using a new local instance of galaxy at my university. I am having problems executing tophat. I have pasted the error below. Can anyone give me a hint on what the problem might be? Funny thing is that the output files are generated and contains some content, but Tophat is unable to complete the job.
"The Galaxy framework encountered the following error while attempting to run the tool:
Traceback (most recent call last): File "/opt/exp_soft/galaxy/srvubugal002/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/opt/exp_soft/galaxy/srvubugal002/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1124, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/opt/exp_soft/galaxy/srvubugal002/galaxy-dist/lib/galaxy/datatypes/binary.py", line 244, in set_meta proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory"