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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Attachment: velvet.patch
Description: Binary data

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