While I've got you on the line, do you know why enabling the real user method 
blanks out the jobName for the PBS job?  The jobName is set if the jobs are 
submitted as the Galaxy user.

David

On Oct 3, 2012, at 11:03 AM, Nate Coraor wrote:

> On Oct 3, 2012, at 10:06 AM, David Hoover wrote:
> 
>> 
>>> This script is used multiple times, so you might want to make sure that 
>>> this change won't cause files to become readable that you would prefer 
>>> remain unreadable.
>> 
>> From the log output, it looks like files are chmod'd to the user, then later 
>> back to the Galaxy user.  Is there somewhere else that isn't logged?
> 
> Hi David,
> 
> It chowns the entire working directory, I double checked and I don't see 
> anywhere else it runs.  But after looking at the code again, I'm surprised 
> this fix works since it shouldn't touch anything in new_file_path.
> 
>> 
>>> Since you mention Apache uploading, what are you using for Apache to handle 
>>> the uploads?
>> 
>> I don't know, whatever the default mechanism.  I'm not using nginx.
> 
> This would just upload straight through to Galaxy without any special 
> handling by Apache.  Tempfiles are created by Galaxy's internal webserver via 
> the FieldStorage monkeypatch in lib/galaxy/web/framework/base.py
> 
> --nate
> 
>> 
>> David


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