Question: Error when trying to install SOME tools from shedtools on galaxy on biolinux 8
0
gravatar for thondeboer
4.2 years ago by
thondeboer0
thondeboer0 wrote:

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.

It seems to happen only to some packages from the shedtools, not all.

This one gives me the error:

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

 

This one works fine:

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

 

Any ideas?

 

Thon

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 - : '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

biolinux shedtool • 1.9k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by thondeboer0
1

Not sure off the top of my head, but is it possible for you to check the revision of the galaxy installed on your biolinux 8 box, or is it still shipped sans-hg?

ADD REPLYlink written 4.2 years ago by Dannon Baker3.7k

Yep...no Mercurial

ADD REPLYlink written 4.2 years ago by thondeboer0

Well, that definitely makes it a little more difficult to update, or even know what we're dealing with.  If it were me, I'd try to either reproduce the issue on a non-biolinux install, or update the biolinux install 'manually' by dropping a fresh hg clone on top of it.  If you choose the latter, I'd definitely recommend backing up the galaxy install (or just snapshot the VM) first.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Dannon Baker3.7k
0
gravatar for thondeboer
4.2 years ago by
thondeboer0
thondeboer0 wrote:

Yeah, I was hoping to avoid that..Whole point of the BioLinux was that you don't have to mess with individual packages etc.

They have setup Galaxy quite differently from the standard way (it's a service etc., nicely done) so tricky to wipe and clobber with a fresh install

ADD COMMENTlink written 4.2 years ago by thondeboer0
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