On Feb 20, 2013, at 2:37 PM, Anthonius deBoer wrote:

> Ah...Found what root squashing is and yes, that is turned on our isilon 
> system...
> 
> So out of luck I take it? We need to chown? we cannot fake the submission 
> name in another way ;)

Galaxy must have a way to make the job working directory writable for the user 
that the job is running as.  If this means logging in to another system via ssh 
that *does* have the ability to change ownership, then you can do that.  The 
method is completely customizable because you can set the chown script to 
anything that works for you.

However, some means of doing this that is appropriate for your environment has 
to exist for Galaxy to perform it.  That said, you might be able to get away 
with having the script make the working directory world-writeable instead of 
owned by the real user.

--nate

> 
> Thanks
> 
> Thon
> 
> On Feb 20, 2013, at 10:32 AM, Anthonius deBoer <thondeb...@me.com> wrote:
> 
>> I cannot run chown even as a sudo command...Same error...
>> What is root squashing? I am reading on the internet that it is very common 
>> not to allow users to change the ownership of files...
>> 
>> 
>> Thon
>> On Feb 20, 2013, at 05:52 AM, Nate Coraor <n...@bx.psu.edu> wrote:
>> 
>>> On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote:
>>> 
>>> > Hi,
>>> > 
>>> > I am trying to setup my galaxy system to allow jobs to be submitted as 
>>> > the real user, since people want to keep an eye on their job on the 
>>> > cluster sometimes and they have no ideas which ones are theirs…
>>> > 
>>> > I tried the approach on the wiki here:
>>> > 
>>> > http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?highlight=%28submit%29%7C%28jobs%29%7C%28as%29%7C%28user%29#Submitting_Jobs_as_the_Real_User
>>> > 
>>> > but unfortunately, the CHOWN command is not allowed, not even as a sudo 
>>> > user…
>>> > Probably has to do with the fact that we run our cluster from an isilon 
>>> > system, which I assume is pretty typical…
>>> > 
>>> > The job was actually successfully submitted as the intended user, so that 
>>> > part works, but if we can just get it to work without having to rely on 
>>> > chown that would be awesome…
>>> > 
>>> > Can someone point me in the right direction?
>>> 
>>> Hi Thon,
>>> 
>>> If you run the command from the command line, what results do you get?
>>> 
>>> /usr/bin/sudo -E scripts/external_chown_script.py 
>>> /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148
>>>  svcgalaxy 10000
>>> 
>>> Note that external_chown_script.py can be modified as necessary to allow 
>>> you to change ownership in whatever way is appropriate for your site. Since 
>>> it should just be an NFS mount, as long as root squashing is not enabled 
>>> and your svcgalaxy user has sudo permission to run this script, it should 
>>> succeed.
>>> 
>>> --nate
>>> 
>>> > 
>>> > Here’s the error…
>>> > 
>>> > galaxy.jobs.runners.local DEBUG 2013-02-19 19:35:31,524 execution of 
>>> > external set_meta for job 148 finished
>>> > galaxy.jobs DEBUG 2013-02-19 19:35:31,576 (148) Changing ownership of 
>>> > working directory with: /usr/bin/sudo -E scripts/external_chown_script.py 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148
>>> >  svcgalaxy 10000
>>> > galaxy.jobs ERROR 2013-02-19 19:35:31,653 (148) Failed to change 
>>> > ownership of 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148,
>>> >  failing
>>> > Traceback (most recent call last):
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", 
>>> > line 343, in finish
>>> > self.reclaim_ownership()
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", 
>>> > line 916, in reclaim_ownership
>>> > self._change_ownership( self.galaxy_system_pwent[0], str( 
>>> > self.galaxy_system_pwent[3] ) )
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", 
>>> > line 902, in _change_ownership
>>> > assert p.returncode == 0
>>> > AssertionError
>>> > galaxy.jobs DEBUG 2013-02-19 19:35:31,722 fail(): Moved 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148/galaxy_dataset_332.dat
>>> >  to 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/files/000/dataset_332.dat
>>> > galaxy.datatypes.metadata DEBUG 2013-02-19 19:35:31,924 Cleaning up 
>>> > external metadata files
>>> > 
>>> > Thanks
>>> > 
>>> > Thon
>>> > ___________________________________________________________
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>>> 
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