SSL certificate errors

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SSL certificate errors

Matthias Bernt
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%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
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%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/')],
'changeset_revisions=9ba8ebb636f4&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=d5dd1c5d2070513e&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,
[hidden email], 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/

To search Galaxy mailing lists use the unified search at:
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Re: SSL certificate errors

Marius van den Beek

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 <[hidden email]> 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%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
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%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/')], 'changeset_revisions=9ba8ebb636f4&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=d5dd1c5d2070513e&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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], 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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: SSL certificate errors

Matthias Bernt
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 <[hidden email]
> <mailto:[hidden email]>> 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>,
>     [hidden email] <mailto:[hidden email]>, 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/>
>
>
--

-------------------------------------------
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,
[hidden email], 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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

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