Hi John,
Here is what I've tracked down this morning. On the off chance this seems
wildly off the mark I don't know much about python or galaxy. I am drinking
fancy coffee though ;)
I did confirm all the folders are world executable. The upload is running as a
local job, not a cluster job.
I put some debugging code into galaxy-dist/lib/galaxy/datatypes/registry.py and
the chmod in that code block is not called for the uploaded file.
I made an edit to scripts/external_chown_script.py
I added the line:
os.system('chmod 0644 %s' %(path))
that made the uploaded file world readable and pushed me to the next error that
reads:
galaxy.jobs ERROR 2014-06-11 09:33:31,562 fail(): Missing output file in
working directory:
[Errno 13] Permission denied:
'/panfs/storage.local/software/galaxy-dist/database/job_working_directory/000/8/galaxy_dataset_8.dat'
It looks like the problem is with the permissions on the newly created folder
(8 in this case)
-bash-4.1$ ls -l database/job_working_directory/000/
total 64
drw-r--r-- 2 galaxy galaxy 4096 Jun 11 09:33 8
The folder is does not have execute permissions turned on. Could someone point
me to the block of code where the mkdir is run? Or of course if there is some
setting I've missed some place please let me know!
Thanks for the help.
Donny
FSU RCC
-----Original Message-----
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: Wednesday, June 11, 2014 9:30 AM
To: Shrum, Donald C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] upload problems
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 <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.
>
> --Donny
>
> -----Original Message-----
> From: John Chilton [mailto:jmchil...@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/e2b761a9b1d6d41d
> b71b28df8b62862c7c300eba/lib/galaxy/datatypes/registry.py?at=default#c
> l-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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