On Oct 2, 2012, at 1:39 PM, David Hoover wrote:
> 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.
Hi David,
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.
Since you mention Apache uploading, what are you using for Apache to handle the
uploads?
--nate
>
> 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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>
>
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