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> 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 [^]
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