Hi Matthias, this looks like your python installation does not know how to verify SSL certificates. Redhat have a nice section on troubleshooting that here: https://access.redhat.com/articles/2039753 I can get your error by specifying a nonexsting cert: |mvandenb@Mariuss-MacBook-Pro:~/src/readtagger/readtagger (master)*$ SSL_CERT_FILE=/does_not_exist python ~/urllib2_test.py https://usegalaxy.org Traceback (most recent call last): File "/Users/mvandenb/urllib2_test.py", line 10, in <module> urllib2.urlopen(req) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 429, in open response = self._open(req, data) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 447, in _open '_open', req) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1241, in https_open context=self._context) File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1198, in do_open raise URLError(err) urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> | Hope that helps, Marius ​ On 18 April 2017 at 17:13, Matthias Bernt <m.bernt(a)ufz.de <mailto:m.bernt@ufz.de>> wrote: Dear list, Currently I get SSL certificate errors when I try to install a tool in Galaxy. I also get the same error when I try to use the galaxy-tools ansible role (when debugging this I thought this might be because my local server is on http, since the error appeared seemingly when a message was posted to the local server -- but I'm not entirely sure). I'm also missing the "Manage installed tools" link in the admin area (but maybe this is expected in a fresh install?). Thanks a lot. Best, Matthias This is the stack trace when I try to install through the web frontend: 141.65.27.89 - - [18/Apr/2017:14:58:19 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu <http://2Ftoolshed.g2.bx.psu.edu>%2F HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0" Error - <class 'urllib2.URLError'>: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> URL: http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revi... <http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revi... File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in __call__ return self.handle_request( environ, start_response ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 193 in handle_request body = method( trans, **kwargs ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1035 in prepare_for_install raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py', line 1488 in url_get response = urlopener.open( full_url ) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 429 in open response = self._open(req, data) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 447 in _open '_open', req) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 407 in _call_chain result = func(*args) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 1241 in https_open context=self._context) File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py', line 1198 in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)> CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa' HTTP_DNT: '1' HTTP_HOST: 'bioinf2-dev:8080' HTTP_UPGRADE_INSECURE_REQUESTS: '1' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0' PATH_INFO: '/admin_toolshed/prepare_for_install' QUERY_STRING: 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu <http://2Ftoolshed.g2.bx.psu.edu>%2F' REMOTE_ADDR: '141.65.27.89' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x7f2dd8bb5190> controller_action_key: u'web.admin_toolshed.prepare_for_install' is_api_request: False paste.cookies: (<SimpleCookie: galaxysession='5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'>, 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f2dd8bb5110> paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f2dd875fe10> paste.parsed_querystring: ([('changeset_revisions', '9ba8ebb636f4'), ('repository_ids', 'd5dd1c5d2070513e'), ('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/') <https://toolshed.g2.bx.psu.edu/';)>], 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu <http://2Ftoolshed.g2.bx.psu.edu>%2F';) 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: '7599ea98244711e7941208002755efa5' webob._parsed_query_vars: (GET([(u'changeset_revisions', u'9ba8ebb636f4'), (u'repository_ids', u'd5dd1c5d2070513e'), (u'tool_shed_url', u'https://toolshed.g2.bx.psu.edu/';)] <https://toolshed.g2.bx.psu.edu/')%5D>), 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu <http://2Ftoolshed.g2.bx.psu.edu>%2F';) wsgi process: 'Multithreaded' ------------------------------------------------------------ -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.bernt(a)ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de> Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann ------------------------------------------- ___________________________________________________________ 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: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>