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'
I uninstalled MACS and MACS2 and it did not fix the problem.
this comment has been removed because the error was fixed (see below)
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()*