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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