Dave,

I upgraded the galaxy to Sep 7 release. The KeyError error has gone as
expected.

But the deferred_job_queue error persists. We are running galaxy in the
cluster (SGE) here. Is it possible that Manage local data need to be
configured in the cluster env?

Regards,
Derrick

On Mon, Sep 10, 2012 at 10:59 PM, Dave Bouvier <d...@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<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 <klin...@gmail.com
>> <mailto:klin...@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>[^
>>     
>> <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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