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 <[email protected]>
> Date: October 2, 2012 1:21:02 PM EDT
> To: Oleksandr Moskalenko <[email protected]>
> Cc: [email protected]
> 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 <[email protected]> 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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