So the permissions on these files seem fine right. That is odd.
Next things I would check are that each directory leading up to
/panfs/storage.local/scratch/galaxy-data/ is world executable and that
the whole thing (/panfs/storage.local/scratch/galaxy-data/) is mounted
and with the same permissions on the cluster worker nodes.
If users can indeed read that file - the error message must be
misleading some how (that would not be entirely surprising).
On Tue, Jun 10, 2014 at 4:48 PM, Shrum, Donald C <dcsh...@admin.fsu.edu> wrote:
> Hi Jon and thanks for the reply. I am attempting to run jobs as the real
> user as jobs will go to our HPC cluster. This will be an enterprise server.
> /panfs/storage.local/scratch/galaxy-data/ is world writable-
> drwxrwxrwx 4 galaxy galaxy 4096 May 7 09:08 galaxy-data
> as is tmp
> -bash-4.1$ ls -l /panfs/storage.local/scratch/galaxy-data/
> total 160
> drwxrwxrwx 2 galaxy galaxy 20480 Jun 10 17:00 tmp
> I got a little lost on the integrated datatypes configuration file... is that
> an XML file? I'm not sure which file I'm looking for and I'm new to galaxy.
> -----Original Message-----
> From: John Chilton [mailto:jmchil...@gmail.com]
> Sent: Tuesday, June 10, 2014 5:33 PM
> To: Shrum, Donald C
> Cc: email@example.com
> Subject: Re: [galaxy-dev] upload problems
> 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
> - 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?
> On Tue, Jun 10, 2014 at 4:10 PM, Shrum, Donald C <dcsh...@admin.fsu.edu>
>> 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
>> Traceback (most recent call last):
>> line 394, in <module>
>> line 369, in __main__
>> registry.load_datatypes( root_dir=sys.argv, config=sys.argv )
>> line 97, in load_datatypes
>> tree = galaxy.util.parse_xml( config )
>> 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:
>> -bash-4.1$ ls -l
>> -rw------- 1 dcshrum dcshrum 317 Jun 10 16:30
>> It does not look like galaxy is using sudo to run the script. Suggestions
>> to work this out?
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