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
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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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