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.be...@ufz.de
<mailto: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=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.be...@ufz.de <mailto:m.be...@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.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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Description: S/MIME Cryptographic Signature

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