Was velveth working prior to the patch (i.e. is it okay to use
extra_files_path on outputs?) or does some more work need to be done
at the infrastructure level to copy output extra files over in
run-as-user mode?

-John

On Thu, Dec 6, 2012 at 4:52 AM, Andreas Kuntzagk
<andreas.kuntz...@mdc-berlin.de> wrote:
> Ok,
>
> while velveth seems to work now, if I put the result into velvetg I get
> another error:
>
> Traceback (most recent call last):
>   File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
> 175, in queue_job
>     job_wrapper.prepare()
>   File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 184, in
> prepare
>     self.command_line = self.tool.build_command_line( param_dict )
>   File "/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2424,
> in build_command_line
>     command_line = fill_template( self.command, context=param_dict )
>   File "/data/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in
> fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py",
> line 84, in respond
> NotFound: cannot find 'files_path' while searching for 'input.files_path'
>
> Andreas
>
>
> On 06.12.2012 10:52, Andreas Kuntzagk wrote:
>>
>> 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
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
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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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