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
