Thanks John,

The long term vision you outline makes a lot of sense; I've just
added a note to the wiki to try to help anyone else running into this:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?action=diff&rev1=51&rev2=52

Peter

On Mon, Jan 25, 2016 at 5:27 PM, John Chilton <jmchil...@gmail.com> wrote:
> Peter -
>
> Nate and I are in agreement that the goal is to eliminate that
> directory, so I don't want to put effort into automating its creation.
>
> https://github.com/galaxyproject/galaxy/issues/1576
>
> If you wish to open a PR that does this though, I would be happy to
> merge this. The best place to ensure this directory exists is in the
> drmaa runner where it is being used.
>
> -John
>
>
>
> On Mon, Jan 25, 2016 at 4:20 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> 
>> wrote:
>>> Hello all,
>>>
>>> We're currently looking at changing our Galaxy setup to link user accounts
>>> with Linux user accounts for better cluster integration (running jobs as the
>>> actual user on SGE). As part of this, we've tried setting up a fresh
>>> installation on a new VM which has thrown up some issues.
>>>
>>> [snip]
>>
>> We eventually got Galaxy to talk to SGE and submit jobs successfully
>> as the individual user's Linux account, with external_chown_script.py
>> being called to handle ownership of the files.
>>
>> One small stumbling block was missing the cluster_files_directory directory.
>> https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample
>> says:
>>
>> # If using a cluster, Galaxy will write job scripts and stdout/stderr to this
>> # directory.
>> #cluster_files_directory = database/pbs
>>
>> According the the current code, this is still the default value being used:
>>
>> https://github.com/galaxyproject/galaxy/blob/274af50792aaaf367520c22d7c13e22e70000d4d/lib/galaxy/config.py#L170
>>
>> However, Galaxy itself did not seem to create the cluster_files_directory
>> directory - and there doesn't seem to be a ready-made pbs folder in the
>> git repository. Should that happen automatically?
>>
>> At one stage, run.sh would create database/files and database/tmp -
>> I'm note sure what that happens now:
>>
>> https://github.com/galaxyproject/galaxy/commit/4d720d63c631862778e54bd68c4e375438ba3ea5
>> https://github.com/galaxyproject/galaxy/commit/7560751dc87492471880c82b00857af12565c06b
>>
>> Peter
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