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?



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