Error trying to install from shedtool into Galaxy on Biolinux 8

[thondeboer]

Just got Biolinux 8 and trying to install some tools in GALAXY from the toolshed, but seeing this error in the log after I press the INSTALL button in the UI

Any ideas?

192.168.50.112 - - [15/Aug/2014:16:38:05 -0600] "GET /galaxy/admin_toolshed/browse_tool_shed?tool_sh
ed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://192.168.50.140:8080/galaxy/adm
in_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (K
HTML, like Gecko) Chrome/36.0.1985.143 Safari/537.36"
tool_shed.tool_shed_registry DEBUG 2014-08-15 16:38:15,410 Invalid url 'https://toolshed.g2.bx.psu.e
du/' received by tool shed registry's password_manager_for_url method.
192.168.50.112 - - [15/Aug/2014:16:38:15 -0600] "GET /galaxy/admin_toolshed/prepare_for_install?tool
_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=997cccce43caabe7&changeset_revisions=16ecf2
5d521f HTTP/1.1" 500 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML
, like Gecko) Chrome/36.0.1985.143 Safari/537.36"
Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'strip'
URL: http://192.168.50.140:8080/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=https://tool
shed.g2.bx.psu.edu/&repository_ids=997cccce43caabe7&changeset_revisions=16ecf25d521f
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/usr/lib/galaxy-server/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/usr/lib/galaxy-server/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __ca
ll__
  return self.application(environ, start_response)
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 132 in __call__
  return self.handle_request( environ, start_response )
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 372 in decorator
  return func( self, trans, *args, **kwargs )
File '/usr/lib/galaxy-server/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 983 in p
repare_for_install
  includes_tool_dependencies )
File '/usr/lib/galaxy-server/lib/tool_shed/util/common_install_util.py', line 97 in get_dependencies
_for_repository
  repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repos
itory_owner, changeset_revision )
File '/usr/lib/galaxy-server/lib/tool_shed/util/shed_util_common.py', line 1036 in get_repository_fo
r_dependency_relationship
  ( name, owner, changeset_revision ) )
File '/usr/lib/galaxy-server/lib/tool_shed/util/shed_util_common.py', line 1867 in url_join
  parts.append( arg.strip( '/' ) )
AttributeError: 'NoneType' object has no attribute 'strip'


CGI Variables

[thondeboer]

A little more info on this issue

I have also tried to get GALAXY to run with a POSTGRES database, since the BioLinux 8 site states there is some automatic way to get galaxy to run with postgres, but there is no information their site, so I googled it and found this for BioLinux 7 which I applied

http://nebclists.nerc.ac.uk/pipermail/bio-linux-announce/2014-January/000016.html

sudo apt-get install galaxy-server-pg-database

Not sure if that was the way to do it (It was for BL7) but that was the only information I found (BioLinux documentation is quite minimal)

[thondeboer]

I have some more information on this error.
It seems to happen with most of the package on the shedtool, but not all.
It happens to this one:

https://toolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?repository_ids=c45d6c51a4fcfc6c&changeset_revisions=ab1f60c26526

But not this one:

https://toolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?repository_ids=57bdf6799bfc0837&changeset_revisions=eb166cebbe3c

[swebb]

Did you have any luck figuring this out. I am having the same problem.