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.be...@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=9ba8
> ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%
> 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?c
> hangeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d20705
> 13e&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/gal
> axy/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+x
> ml,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=5d9fe20b2f75201
> eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'
>   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=9ba8ebb63
> 6f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%
> 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='5d9fe20b2f75201
> eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'>,
> 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7d
> a2cc7e5bd9aff8a0eb130e333f3419e10fa')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPExce
> ption'>]
>   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/')], 'changeset_revisions=9ba8ebb63
> 6f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%
> 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/')]),
> 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d207
> 0513e&tool_shed_url=https%3A%2F%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,
> m.be...@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
> -------------------------------------------
>
>
> ___________________________________________________________
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