Derrick

On Mon, Sep 10, 2012 at 10:59 PM, Dave Bouvier <dave@bx.psu.edu> wrote:

Derrick,

The deferred_job_queue instance in the job manager object is only instantiated when the enable_beta_job_managers variable is set to True. Is it possible that your previous setting of that variable was somehow reverted?

The KeyError error you mentioned in your previous should be fixed in the latest -dist and -central revisions.

--Dave B.

On 9/9/12 21:20:44.000, Derrick Lin wrote:

Hi guys,

I found that the problematic loc files were created by CloudBioLinux and
point to the reference indexes downloaded by CloudBioLinux script. I
suspect that Manage Local Data cannot recognize the file structure
created by CloudBioLinux?

Anyhow, I removed all the loc files from CloudBioLinux, then Manage
Local Data can run now. Soon after I tried to download the bowtie hg18
from ucsc, I was given another error caused by "deferred job queue":

URL: http://129.94.136.11:8080/galaxy_dev/data_admin/download_build
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py',
line 184 in decorator
return func( self, trans, *args, **kwargs )
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py',
line 199 in download_build
jobid =
trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job(
trans, url, dbkey, longname, indexers )
AttributeError: 'JobManager' object has no attribute 'deferred_job_queue'

Anyone can give some hints about what was going on?

Regards,
Derrick

On Fri, Sep 7, 2012 at 4:26 PM, Derrick Lin <klin938@gmail.com
<mailto:klin938@gmail.com>> wrote:

Hi guys,

I enabled the tool with enable_beta_job_managers = True, server runs
fine. But after I clicked on Manage local data, it gave the
following error:

URL:
http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data [^
<http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data>]

File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py',
line 184 in decorator
return func( self, trans, *args, **kwargs )
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py',
line 47 in manage_data
genomes[ dbkey ][ table ] = dict( state='Generated',
style=self.jobstyles[ 'done' ] )
KeyError: 'phix'

I tried to fix it by commenting out all the phix entries in all .loc
files. Then it gave the same error but this time caused by "hg18". I
think it must have something to do with builts.txt,
manual_builts.txt and the loc files?

Thanks
Derrick

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