Re: [galaxy-dev] Galaxy broken after update to 16.01

2016-02-09 Thread Peter van Heusden 
Mattias, what does your supervisord config look like? Specifically, does it
contain an environment variable to direct the Galaxy handler to the correct
virtualenv?

Peter

On 9 February 2016 at 16:03, Matthias De Smet 
wrote:

> 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 
> from galaxy.webapps.galaxy.buildapp import app_factory
>   File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in 
> import galaxy.app
>   File "lib/galaxy/app.py", line 9, in 
> import galaxy.queues
>   File "lib/galaxy/queues.py", line 9, in 
> 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 
> from .abstract import MaybeChannelBound, Object
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py",
> line 12, in 
> from .connection import maybe_channel
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py",
> line 19, in 
> from kombu import exceptions
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py",
> line 12, in 
> from amqp import ChannelError, ConnectionError, ResourceError
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py",
> line 34, in 
> from .connection import Connection  # noqa
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py",
> line 40, in 
> from .transport import create_transport
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py",
> line 21, in 
> import ssl
>   File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line
> 97, in 
> 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
>
>
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[galaxy-dev] Galaxy broken after update to 16.01

2016-02-09 Thread Matthias De Smet 
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 
from galaxy.webapps.galaxy.buildapp import app_factory
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in 
import galaxy.app
  File "lib/galaxy/app.py", line 9, in 
import galaxy.queues
  File "lib/galaxy/queues.py", line 9, in 
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 
from .abstract import MaybeChannelBound, Object
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py", 
line 12, in 
from .connection import maybe_channel
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py",
 line 19, in 
from kombu import exceptions
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py",
 line 12, in 
from amqp import ChannelError, ConnectionError, ResourceError
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py", 
line 34, in 
from .connection import Connection  # noqa
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py",
 line 40, in 
from .transport import create_transport
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py", 
line 21, in 
import ssl
  File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line 97, 
in 
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

___
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  https://lists.galaxyproject.org/

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