Question: Python Error? unexpected keyword argument [fixed]
0
gravatar for Brian Griffiths
2.6 years ago by
United States
Brian Griffiths20 wrote:

Hi,

I recently started getting the following error whenever I try to do anything. The last things I did were install some tools from the toolshed (MACS and MACS2). Those worked fine. Then I ran Tophat on some files. When I tried to run cufflinks, I started getting the error. When I try to upload a file I get the error. It seems to trigger anytime a dataset is created. I'm not exactly sure where the error is occuring, and I don't want to go through the trouble of uninstalling MACS/MACS2 if that's not where the problem is, because things were working fine after that. I have tried restarting my computer and upgrading everything. Hope somebody understands python more than I do.

Traceback (most recent call last):

File "/home/user/galaxy/tools/data_source/upload.py", line 10, in <module> import galaxy.model

File "/home/user/galaxy/lib/galaxy/model/__init__.py", line 9, in <module> eggs.require("pexpect")

File "/home/user/galaxy/lib/galaxy/eggs/__init__.py", line 479, in require return c[req.project_name].require()

File "/home/user/galaxy/lib/galaxy/eggs/__init__.py", line 275, in require pkg_resources.working_set.add( dist )

File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 758, in add

TypeError: _insert_on() got an unexpected keyword argument 'replace'

software error galaxy • 2.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Brian Griffiths20

I uninstalled MACS and MACS2 and it did not fix the problem.

ADD REPLYlink written 2.6 years ago by Brian Griffiths20

this comment has been removed because the error was fixed (see below)

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Brian Griffiths20

If I try to install samtools to get rid of that error in the beginning, I get another error:

THIS ERROR WAS FIXED (see comment)

object of type 'bool' has no len(), which I seem to get a lot when I watch the terminal. galaxy.tools.toolbox.base DEBUG 2016-04-19 12:51:30,540 Appending to tool panel section: Sam Tools warning: toolshed.g2.bx.psu.edu certificate with fingerprint 54:1e:bc:3d:37:34:25:8a:77:35:ce:d9:2d:48:88:65:27:d0:0a:76 not verified (check hostfingerprints or web.cacerts config setting) 127.0.0.1 - - [19/Apr/2016:12:51:31 -0400] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0" 127.0.0.1 - - [19/Apr/2016:12:51:25 -0400] "POST /admin_toolshed/manage_repositories HTTP/1.1" 500 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:45.0) Gecko/20100101 Firefox/45.0" Error - <type 'exceptions.typeerror'="">: object of type 'bool' has no len() URL: http://127.0.0.1:8080/admin_toolshed/manage_repositories File '/home/user/galaxy/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/user/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/user/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/user/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/user/galaxy/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, *kwargs ) File '/home/user/galaxy/lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, args, *kwargs ) File '/home/user/galaxy/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 684 in manage_repositories reinstalling=reinstalling, File '/home/user/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 844 in install_repositories reinstalling=reinstalling ) File '/home/user/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 894 in install_tool_shed_repository reinstalling=reinstalling ) File '/home/user/galaxy/lib/tool_shed/galaxy_install/install_manager.py', line 530 in __handle_repository_contents irmm.generate_metadata_for_changeset_revision() File '/home/user/galaxy/lib/tool_shed/metadata/metadata_generator.py', line 443 in generate_metadata_for_changeset_revision metadata_dict ) File '/home/user/galaxy/lib/tool_shed/metadata/metadata_generator.py', line 668 in generate_tool_metadata elif len( values ) == 1: TypeError: object of type 'bool' has no len()*

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Brian Griffiths20
1
gravatar for Brian Griffiths
2.6 years ago by
United States
Brian Griffiths20 wrote:

This error was fixed with this solution:

GATK 2.8 stuck on cloning, repair error : object of type 'bool' has no len()

ADD COMMENTlink written 2.6 years ago by Brian Griffiths20
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