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
On Thu, Dec 6, 2012 at 4:52 AM, Andreas Kuntzagk
while velveth seems to work now, if I put the result into velvetg I get
Traceback (most recent call last):
File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
175, in queue_job
File "/data/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 184, in
self.command_line = self.tool.build_command_line( param_dict )
File "/data/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2424,
command_line = fill_template( self.command, context=param_dict )
File "/data/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in
return str( Template( source=template_text, searchList=[context] ) )
line 1004, in __str__
return getattr(self, mainMethName)()
line 84, in respond
NotFound: cannot find 'files_path' while searching for
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.
> On 05.12.2012 13:40, Andreas Kuntzagk wrote:
>> 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?
>>> (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:
>>> (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 <om(a)hpc.ufl.edu>
>>>> On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk
>>>> <andreas.kuntzagk(a)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.
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