Trying out a local instance of Galaxy. Small files can be uploaded with 
"browse.." but this works only for files under 2Gb. Is there a folder in a 
local copy of galaxy-dist where I can copy a large file and have it show up in 
the Get Data/Upload File/Files uploaded via FTP window so that I can properly 
get it into the local history? Copying it directly into the database seemed not 
to work, it didn't show up anywhere.

Gerald 


>________________________________
> From: Rodolfo Aramayo <raram...@tamu.edu>
>To: Dave Bouvier <d...@bx.psu.edu> 
>Cc: galaxy-...@bx.psu.edu; Rodolfo Aramayo <raram...@tamu.edu> 
>Sent: Monday, August 5, 2013 2:07 PM
>Subject: Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
>  
>
>Dave,
>
>Also, when I click on:
>
>"Get repository update"
>
>I get the following error:
>##########################################################
>URL: 
>http://galaxy.tamu.edu/admin_toolshed/check_for_updates?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
>File 
>'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>line 149 in __call__
>  app_iter = self.application(environ, sr_checker)
>File 
>'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>line 84 in __call__
>  return self.application(environ, start_response)
>File 
>'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>line 633 in __call__
>  return self.application(environ, start_response)
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>line 132 in __call__
>  return self.handle_request( environ, start_response )
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>line 190 in handle_request
>  body = method( trans, **kwargs )
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>line 221 in decorator
>  return func( self, trans, *args, **kwargs )
>File 
>'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>line 202 in check_for_updates
>  repository = suc.get_installed_tool_shed_repository( trans, repository_id )
>File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
>line 515 in get_installed_tool_shed_repository
>  return trans.sa_session.query( trans.model.ToolShedRepository ).get(
>trans.security.decode_id( id ) )
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
>line 60 in decode_id
>  return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) )
>ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'
>
>##########################################################
>
>Thanks
>
>--R
>
>On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> Rodolfo,
>>
>> In order to simplify tracking down this issue, could you provide the
>> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
>> revision, execute the following command in your galaxy root directory:
>>
>> hg id
>>
>> To clarify, our understanding is that you installed the ncbi_blast_plus
>> repository from the main tool shed, and it installed correctly. You then
>> uninstalled the repository, and it also uninstalled properly. You then
>> attempted to reinstall the repository, and encountered the error message
>> cited in your email.
>>
>> Can you confirm the above?
>>
>> We further understand that the repository is stuck in the 'installing'
>> state. What options are available from the popup menu next to the
>> ncbi_blast_plus repository on the manage installed repositories page? If
>> 'Deactivate or uninstall' is available, can you try uninstalling again, and
>> see if that functions correctly?
>>
>>    --Dave B.
>>
>>
>> On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
>>>
>>> People,
>>>
>>> I successfully installed NCBI_Blast_Plus from the toolshed
>>> The tool, however, failed to work giving the following error:
>>>
>>> Fatal error: Exit code 255 ()
>>> Error: NCBI C++ Exception:
>>>
>>> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
>>> line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
>>> Attempt to access NULL pointer.
>>>
>>> I then tried uninstalling/reinstalling the tool
>>>
>>> However I now get an eternal 'installing' grey message and when I
>>> click 'manage the repo' I get:
>>>
>>> #########
>>>
>>> URL:
>>> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
>>> File
>>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>>> line 149 in __call__
>>>    app_iter = self.application(environ, sr_checker)
>>> File
>>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>>> line 84 in __call__
>>>    return self.application(environ, start_response)
>>> File
>>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>>> line 633 in __call__
>>>    return self.application(environ, start_response)
>>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>>> line 132 in __call__
>>>    return self.handle_request( environ, start_response )
>>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>>> line 190 in handle_request
>>>    body = method( trans, **kwargs )
>>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>>> line 221 in decorator
>>>    return func( self, trans, *args, **kwargs )
>>> File
>>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>>> line 561 in manage_repository
>>>    repository = suc.get_installed_tool_shed_repository( trans,
>>> repository_id )
>>> File
>>> '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
>>> line 515 in get_installed_tool_shed_repository
>>>    return trans.sa_session.query( trans.model.ToolShedRepository ).get(
>>> trans.security.decode_id( id ) )
>>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
>>> line 60 in decode_id
>>>    return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip(
>>> "!" ) )
>>> ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'
>>>
>>> #########
>>>
>>> How can I totally uninstall and re-install this tool?
>>>
>>> Thanks
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>    http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>    http://galaxyproject.org/search/mailinglists/
>>>
>>
>___________________________________________________________
>Please keep all replies on the list by using "reply all"
>in your mail client.  To manage your subscriptions to this
>and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
>To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>
>
>    
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