[galaxy-dev] Manage Local data

2013-03-26 Thread Shaun Webb 


Hi I am trying to load the mm10 genome and indexes using the manage  
local data admin feature.


The genome downloads ok and so do the liftOver chain files, however  
the main controller and indexing jobs fail. They just display error,  
is there any way I can find out more about what is happening here and  
what is failing?


Thanks
Shaun Webb
University of Edinburgh

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-11 Thread Derrick Lin 
Hi Dave,

Thanks for the clarification. Our testing shows that the local data manager
works in the vanilla Galaxy (simply hg clone, then run.sh). It failed on
our clustered instance that it has been configured to use multiple web
threads, one job manager and two job handlers.

Local data manager is a great idea, it would be even better if it can fetch
the indexes from the local file system.

Cheers,
Derrick

On Tue, Sep 11, 2012 at 10:31 PM, Dave Bouvier  wrote:

> Derrick,
>
> I have not actually tested the local data manager on CloudBioLinux, but
> that sounds like something worth looking into.
>
> As for the rsync server mentioned in another email, the data manager
> checks our rsync server first, then tries generating indexes if the rsync
> server doesn't have them. However, it will always produce indexes, as I
> decided to allow for the option to regenerate indexes, if the local ones
> had somehow become corrupted.
>
>--Dave B.
>
>
> On 9/11/12 02:03:45.000, Derrick Lin wrote:
>
>> 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 > > 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
>> > 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
>>

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-11 Thread Dave Bouvier 

Derrick,

I have not actually tested the local data manager on CloudBioLinux, but 
that sounds like something worth looking into.


As for the rsync server mentioned in another email, the data manager 
checks our rsync server first, then tries generating indexes if the 
rsync server doesn't have them. However, it will always produce indexes, 
as I decided to allow for the option to regenerate indexes, if the local 
ones had somehow become corrupted.


   --Dave B.

On 9/11/12 02:03:45.000, Derrick Lin wrote:

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 mailto: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

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 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

[^

>]

 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/PW

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-10 Thread Derrick Lin 
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  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 > > 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

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-10 Thread Derrick Lin 
Hi Dave,

The  enable_beta_job_managers is set to true in my universe ini file.
Unless it can be override in somewhere else?

My galaxy hasn't been patched to the Sep release, but will give it a try.

I actually also downloaded the complete pre-built indexes from galaxy's
recent released rsync server. I am wondering if the Manage data tool
recognizes those downloaded indexes and avoid downloading again from uscs
server?

Derrick

On Mon, Sep 10, 2012 at 10:59 PM, Dave Bouvier  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 > > 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.applic

Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-10 Thread Dave Bouvier 

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 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 [^
]
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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Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-09 Thread Derrick Lin 
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  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
>
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[galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-06 Thread Derrick Lin 
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
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in your mail client.  To manage your subscriptions to this
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