Hi all, I'm working with a problem with user uploaded files. After digging through the logs a bit and running the commands on at a time manually I think I've narrowed it to a permissions problem. This was confirmed by just running galaxy as root and the problem went away ;) -bash-4.1$ PYTHONPATH=/panfs/storage.local/software/galaxy-dist/lib/ -bash-4.1$ python /panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py /panfs/storage.local/software/galaxy-dist//panfs/storage.local/scratch/galaxy-data/tmp/tmpSuHquR /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf 6:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/dataset_6_files:/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/6/galaxy_dataset_6.dat Traceback (most recent call last): File "/panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py", line 394, in <module> __main__() File "/panfs/storage.local/software/galaxy-dist/tools/data_source/upload.py", line 369, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) File "/panfs/storage.local/software/galaxy-dist/lib/galaxy/datatypes/registry.py", line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/panfs/storage.local/software/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 859, in parse File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 576, in parse IOError: [Errno 13] Permission denied: '/panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf' -bash-4.1$ ls -l /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf -rw------- 1 dcshrum dcshrum 317 Jun 10 16:30 /panfs/storage.local/scratch/galaxy-data/tmp/tmpYGRnAf It does not look like galaxy is using sudo to run the script. Suggestions to work this out?