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). -John On Tue, Jun 10, 2014 at 4:48 PM, Shrum, Donald C <DCShrum@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.
--Donny
-----Original Message----- From: John Chilton [mailto:jmchilton@gmail.com] Sent: Tuesday, June 10, 2014 5:33 PM To: Shrum, Donald C Cc: galaxy-dev@lists.bx.psu.edu 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 (https://bitbucket.org/galaxy/galaxy-central/annotate/e2b761a9b1d6d41db71b28d...) - 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 <DCShrum@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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