Hi Marius, thanks a lot -- you made my day! The solution was: export SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt Cheers, Matthias On 18.04.2017 17:39, Marius van den Beek wrote:

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@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_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F <http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F> 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@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 -------------------------------------------

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-- ------------------------------------------- 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, m.bernt@ufz.de, 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 -------------------------------------------