You didn't include this context, but I am guessing you are attempting
to run jobs as the "real" user? If not, ignore the rest of the e-mail.

I would generally not recommend running the uploads as "real" user -
it is a complex process but should go relatively quick.

Understand that may not be possible though. So that file is the
integrated datatypes configuration file I believe. There is just one
global copy that gets created with Galaxy boots up - so it cannot be
chown-ed on a per job basis. The thing is that Galaxy should be
modifying it to be world readable
(https://bitbucket.org/galaxy/galaxy-central/annotate/e2b761a9b1d6d41db71b28df8b62862c7c300eba/lib/galaxy/datatypes/registry.py?at=default#cl-811)
- something is going wrong if it is not. Can you verify the file is
644?

That leads me to believe that users don't have read access to the
global temp directory. Can you check if users can read
/panfs/storage.local/scratch/galaxy-data/tmp/? I think they will need
to to use some tools including uploads?

If you cannot make this directory accessible to users - can you change
Galaxy's new_file_path so that it is some directory globally readable?

-John

On Tue, Jun 10, 2014 at 4:10 PM, Shrum, Donald C <dcsh...@admin.fsu.edu> wrote:
> 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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