Found a fix.  The external_chown_script.py script forcibly changes the 
permissions on the file to be world-readable.

diff external_chown_script.py external_chown_script.py.ORIG 
33d32
<     os.system('chmod -R a+r %s' %(path))

Please let me know if this is a bad change or if there is a better change.

David

Begin forwarded message:

> From: David Hoover <hoove...@helix.nih.gov>
> Date: October 2, 2012 1:21:02 PM EDT
> To: Oleksandr Moskalenko <o...@hpc.ufl.edu>
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] submitting jobs as the real user
> 
> No, that's not it.  The galaxy user, as well as all other users, have umask 
> 022 by default.
> 
> I believe the problem is with Apache uploading.  I can't figure out how to 
> reconfigure Apache to set the permissions they way I want them.
> 
> David
> 
> On Oct 2, 2012, at 1:17 PM, Oleksandr Moskalenko wrote:
> 
>> Hi David,
>> 
>> I wonder if the user's umask is the problem.
>> 
>> I set the galaxy user's umask to 022 and our default umask on the cluster is 
>> 0022 for all users.
>> 
>> On Oct 2, 2012, at 12:55 PM, David Hoover <hoove...@helix.nih.gov> wrote:
>> 
>>> I'm playing with the "submitting jobs as the real user" method, and 
>>> immediately ran into a problem.  Uploaded files are created in mode 600, 
>>> owned by the user.  Galaxy then gives an error that the tmp file is not 
>>> readable:
>>> 
>>> IOError: [Errno 13] Permission denied: 
>>> '/spin1/users/galaxy/galaxy2/database/tmp/tmp3KHIDt'
>>> 
>>> Is there any way of changing the permissions on the temporary uploaded file 
>>> to 666?
>>> 
>>> David Hoover
>>> Helix Systems Staff
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> 
> 
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