Hi Zhaozhen, the --config_file argument needs to point to galaxy.ini config so the script can load the database. Galaxy continues to support Python 2.6 and 2.7, I am sorry that this script required 2.7 (or you could `pip install argparse`) - we will look into improving it. Martin, Galaxy Team On Wed, Apr 8, 2015 at 4:09 AM 孙兆朕 <sunzzn502@163.com> wrote:

Hi Martin,

Thanks for the advise. It helped a lot for me to figure out where the problem is. However, there were still error messages there. I tried to run the update_shed_config_path.py script under the /script folder. At first it says there was no module named argparse, then I found out it was the python version problem, which required python 2.7+. Then I updated my python. Then there was another error said there was no module named galaxy.model.tool_shed_install. Then I tried harder, and found out that it was the path problem. I figured out the sys path was in the above folder. Then I copied and pasted the update_shed_config_path.py to the parent folder and seemed solved the problem. Then I run the update_shed_config_path.py and the command somehow run for a while, with the error message No module named _sqlite3. It must be the DB versions and plug-ins, then I fixed the DB. Then finally there came the following message:

usage: update_shed_config_path.py [-h] --config_file CONFIG_FILE --from BAD_FILENAME --to GOOD_FILENAME [--force] update_shed_config_path.py: error: argument --config_file is required

I run the command line in: python2.7 update_shed_config_path.py I wonder if I need some more input for the command line or something? By the way, I hope there would be some advise for the new Galaxy administrtators to know their Python should be 2.7+ and file path issues. When I started to deploy Galaxy last year, the requirement in the web page was Python 2.5 or something lower than 2.6 I used. I think that message need to be updated as well. Thanks in advance,

Yours,

Zhaozhen

argparse

At 2015-04-07 22:43:50, "Martin Čech" <marten@bx.psu.edu> wrote:

Hello Zhaozhen,

this is a known problem. The shed_tool_conf.xml got moved along with other configs into /config folder but unfortunately some tools stored the path absolutely in the DB. You can use the following script (which you should find in the Galaxy /scripts folder):

https://github.com/galaxyproject/galaxy/blob/dev/scripts/update_shed_config_... to update your DB to have the correct path to the config.

Sorry for the inconvenience.

Martin, Galaxy Team

On Tue, Apr 7, 2015 at 10:16 AM 孙兆朕 <sunzzn502@163.com> wrote:

...

Hi all,

I want to update some of my tool plug-in and some problem shows, even if I updated my Galaxy instance to the latest. I suppose it is not related to the version of Galaxy.

The problem occured when I used the administrator's panel and update my plug-in using the "Get updates" option. The next page reports that an internal Server Error has occured and the update was not successful. All the plug-in updates seems had the same problem.

I checked the logs where I get the following message:

CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424' HTTP_HOST: '222.28.163.110' HTTP_REFERER: ' http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E .' HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36' HTTP_X_FORWARDED_FOR: '222.28.170.89' HTTP_X_FORWARDED_HOST: '222.28.163.110' ORGINAL_HTTP_HOST: '127.0.0.1:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/admin_toolshed/update_to_changeset_revision' QUERY_STRING: 'tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 ' REMOTE_ADDR: '222.28.170.89' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.0'

WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xd888510> is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650> paste.parsed_querystring: ([('tool_shed_url', ' https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 ') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'a12a5604dce911e4a05000215e543aa8' webob._parsed_query_vars: (MultiDict([('tool_shed_url', ' https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 ') wsgi process: 'Multithreaded' ------------------------------------------------------------ ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 39438) Traceback (most recent call last): File "/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__ self.finish() File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish self.wfile.flush() File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe ---------------------------------------- 222.28.170.89 - - [07/Apr/2015:13:47:59 +0800] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 HTTP/1.0" 500 - " http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'get' URL: http://222.28.163.110/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, **kwargs ) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, *args, **kwargs ) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1954 in update_to_changeset_revision persist=True ) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 31 in __init__ metadata_dict=metadata_dict, user=None ) File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 60 in __init__ self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } AttributeError: 'NoneType' object has no attribute 'get'

CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch' HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424' HTTP_HOST: '222.28.163.110' HTTP_REFERER: ' http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E .' HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36' HTTP_X_FORWARDED_FOR: '222.28.170.89' HTTP_X_FORWARDED_HOST: '222.28.163.110' ORGINAL_HTTP_HOST: '127.0.0.1:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/admin_toolshed/update_to_changeset_revision' QUERY_STRING: 'tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 ' REMOTE_ADDR: '222.28.170.89' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.0'

WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xd888510> is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650> paste.parsed_querystring: ([('tool_shed_url', ' https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 ') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'a58bb404dce911e481c700215e543aa8' webob._parsed_query_vars: (MultiDict([('tool_shed_url', ' https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url= https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 ') wsgi process: 'Multithreaded' ------------------------------------------------------------

Could you please give me some advise to figure out where the problem is and how to fix it?

Thanks,

Zhaozhen

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