Re: [galaxy-dev] Startup problem after upgrade
Template/root directory is missing from my file-system since last update. I have cloned the repository. It seems to miss too. Is there any problem with the repo ? Thankx. -Message d'origine- De : Adam Brenner [mailto:aebre...@uci.edu] Envoyé : mercredi 3 juillet 2013 07:51 À : Bertrand PITOLLAT Cc : galaxy-dev@lists.bx.psu.edu Objet : Re: [galaxy-dev] Startup problem after upgrade When you updated, did you download all the files? Was their any conflicts during the update? It appears you are missing a file. Cant locate template for uri 'root/index.mako' Run 'hg update'... -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Tue, Jul 2, 2013 at 8:10 AM, Bertrand PITOLLAT bertrand.pitol...@cirad.fr wrote: Hi, I have just upgraded my galaxy instance. When trying to access my galaxy instance home page, I get the following error : 195.221.174.40 - - [02/Jul/2013:15:34:23 +0200] GET / HTTP/1.1 500 - - Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36 Error - class 'mako.exceptions.TopLevelLookupException': Cant locate template for uri 'root/index.mako' URL: http://marmadais.cirad.fr:7090/ File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/middlew are/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/pas te/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/pas te/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py ', line 132 in __call__ return self.handle_request( environ, start_response ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py ', line 190 in handle_request body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/webapps/galaxy/contro llers/root.py', line 39 in index params=kwd ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init_ _.py', line 957 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init_ _.py', line 964 in fill_template_mako template = self.webapp.mako_template_lookup.get_template( filename ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Mako-0.4.1-py2.6.egg/mako/l ookup.py', line 221 in get_template Cant locate template for uri %r % uri) TopLevelLookupException: Cant locate template for uri 'root/index.mako' Any help welcome. Bertrand. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Startup problem after upgrade
Hi, I have just upgraded my galaxy instance. When trying to access my galaxy instance home page, I get the following error : 195.221.174.40 - - [02/Jul/2013:15:34:23 +0200] GET / HTTP/1.1 500 - - Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36 Error - class 'mako.exceptions.TopLevelLookupException': Cant locate template for uri 'root/index.mako' URL: http://marmadais.cirad.fr:7090/ File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/middleware/ error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/r ecursive.py', line 84 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/h ttpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/webapps/galaxy/controller s/root.py', line 39 in index params=kwd ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init__.py ', line 957 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init__.py ', line 964 in fill_template_mako template = self.webapp.mako_template_lookup.get_template( filename ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Mako-0.4.1-py2.6.egg/mako/looku p.py', line 221 in get_template Cant locate template for uri %r % uri) TopLevelLookupException: Cant locate template for uri 'root/index.mako' Any help welcome. Bertrand. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Trouble setting up Galaxy with apache proxy
I used this step by step : https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy to set up galaxy with apache proxy. I added these lines to httpd.conf file : RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/bioinfo/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/bioinfo/galaxy/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:7070$1 [P] And these ones to universe_wsgi.ini : [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy I face a problem with the history panel which always displays : Your history is empty. Click 'Get Data' on the left pane to start . Even if I upload Data, even if I log into galaxy. Here is an output of galaxy logs : 195.221.174.200 - - [13/Apr/2011:16:38:56 +0200] GET /galaxy/tool_runner?tool_id=upload1 HTTP/1.1 200 - http://marmadais.cirad.fr:7070/galaxy/root/tool_menu; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:2.0) Gecko/20100101 Firefox/4.0 galaxy.web.framework DEBUG 2011-04-13 16:39:04,250 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create 195.221.174.200 - - [13/Apr/2011:16:39:04 +0200] POST /galaxy/tool_runner/upload_async_create HTTP/1.1 500 - http://marmadais.cirad.fr:7070/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:2.0) Gecko/20100101 Firefox/4.0 Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'id' URL: http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/ errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.p y', line 80 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexcepti ons.py', line 632 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 65 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py' , line 212 in upload_async_create errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1192 in update_state value, error = check_param( trans, input, incoming_value, context ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 56 in check_param value = param.from_html( value, trans, param_values ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 638 in from_html legal_values = self.get_legal_values( trans, context ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 808 in get_legal_values return set( dbkey for dbkey, _ in trans.db_builds ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 695 in db_builds .filter_by( deleted=False, history_id=self.history.id, extension=len ) AttributeError: 'NoneType' object has no attribute 'id' Any help welcome. Thankx. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/