Galaxy broken after update to 16.01 - galaxy-dev

9 Feb 2016


      Hi all,
We were tracking the galaxy master branch on our local server and are looking to migrate to v16.01.
The galaxy processes are managed bij supervisor as shown here ( https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling).
After updating all dependencies in our venv we tried to restart the server but got the following issue:
Loading paste environment: config:/home/galaxy/galaxy-dist/config/galaxy.ini
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 247, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 271, in loadobj
    global_conf=global_conf)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 296, in loadcontext
    global_conf=global_conf)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 320, in _loadconfig
    return loader.get_context(object_type, name, global_conf)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 458, in get_context
    section)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 517, in _context_from_explicit
    value = import_string(found_expr)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 22, in import_string
    return pkg_resources.EntryPoint.parse("x=" + s).load(False)
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2380, in load
    return self.resolve()
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2386, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "lib/galaxy/web/buildapp.py", line 5, in <module>
    from galaxy.webapps.galaxy.buildapp import app_factory
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>
    import galaxy.app
  File "lib/galaxy/app.py", line 9, in <module>
    import galaxy.queues
  File "lib/galaxy/queues.py", line 9, in <module>
    from kombu import Exchange, Queue, Connection
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/__init__.py", line 67, in __getattr__
    module = __import__(object_origins[name], None, None, [name])
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/entity.py", line 10, in <module>
    from .abstract import MaybeChannelBound, Object
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py", line 12, in <module>
    from .connection import maybe_channel
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py", line 19, in <module>
    from kombu import exceptions
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py", line 12, in <module>
    from amqp import ChannelError, ConnectionError, ResourceError
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py", line 34, in <module>
    from .connection import Connection      # noqa
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py", line 40, in <module>
    from .transport import create_transport
  File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py", line 21, in <module>
    import ssl
  File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line 97, in <module>
    import _ssl             # if we can't import it, let the error propagate
ImportError: /home/galaxy/galaxy-dist/.venv/lib/python2.7/lib-dynload/_ssl.so: undefined symbol: SSL_CTX_set_alpn_protos
So far we have tried:
- rebuilding the venv
- reinstalling python
Funny thing is, when we start the configuration with the “run.sh” script instead of through supervisor everything seems to work just fine.
We’re at a loss, please help!
Thanks!
Matthias