Sorry, I think I had not really restarted galaxy after making the change.
After I changed some logging options in universe_wsgi.ini and restarted it's 
suddenly working.
So I can confirm your fix works.

Thank you for your help.

Andreas

On 05.12.2012 13:40, Andreas Kuntzagk wrote:
Hi,

Does not work for me. I still get the same error.
If you need me to run more test, just email me.

regards, Andreas

On 04.12.2012 18:27, John Chilton wrote:
I don't have a velvet or a submit-jobs-as-user environment setup so I
cannot test this, but it seems like this should have a an easy fix.
Can someone who is experiencing the problem try the attached patch or
has something like this been tried and there is some other problem?

-John

(09:43:01 AM) jmchilton: Is the velvet problem related to something
specific about how velvet runs or do no tools that depend on
extra_files_path work with as-user jobs?
(10:10:31 AM) natefoo: they have to either write to files_path or
extra_files_path, let me find the email...
(10:12:24 AM) natefoo:
http://dev.list.galaxyproject.org/Folder-permissions-after-cluster-run-td4657156.html#a4657219
(10:12:26 AM) mrscribe: Title: Galaxy Development List Archive -
Folder permissions after cluster run (at dev.list.galaxyproject.org)
(11:07:31 AM) jmchilton: Is fixing the velvet problem as simple as
changing extra_files_path to files_path in the wrappers then?

On Tue, Dec 4, 2012 at 9:38 AM, Oleksandr Moskalenko <o...@hpc.ufl.edu> wrote:

On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk <andreas.kuntz...@mdc-berlin.de> 
wrote:

I see that this issue came up before by Oleksandr Moskalenko in October but was 
unresolved then.
Is there a workaround now?

regards, Andreas

The velvet wrapper is not going to be usable for real user jobs until someone 
rewrites it to work
without direct manipulation of files in the database/ tree. No work has been 
done on this nor any
is planned as far as I know.

Regards,

Alex
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--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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