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Question: Problems after upgrading Galaxy to 18.09
0
gravatar for david.a.morais
15 days ago by
david.a.morais • 110
Canada
david.a.morais • 110 wrote:

Hello

I just tried to upgrade my Galaxy instance from 18.05 to 18.09 but I am unable to restart it. Below is the error message I receive when I try to start Galaxy after the upgrade.

 File "/cvmfs/soft.galaxy/v2.1/server/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2349, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "lib/galaxy/web/__init__.py", line 5, in <module>
    from .framework import url_for
  File "lib/galaxy/web/framework/__init__.py", line 5, in <module>
    from . import base
  File "lib/galaxy/web/framework/base.py", line 358, in <module>
    webob.compat.cgi_FieldStorage.make_file = _make_file
AttributeError: 'module' object has no attribute 'cgi_FieldStorage'
VACUUM: unix socket /srv/sock/uwsgi.sock removed

I appreciate any kind of suggestion. Cheers

David
18.09 upgrade galaxy 18.05 • 56 views
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written 15 days ago by david.a.morais • 110
0
gravatar for Jennifer Hillman Jackson
15 days ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

What command/method did you use to upgrade? Is Galaxy running inside a virtualenv?

I also started a conversation at the Galaxy Gitter channel to get some developer feedback. They may reply here or there. Please feel free to join in. Sometimes it is easier/quicker to troubleshoot admin issues in a chat format: https://gitter.im/galaxyproject/Lobby?at=5beb3254e0fd6b4360eaba4b
ADD COMMENT • link modified 15 days ago • written 15 days ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

Yes, Galaxy was running inside a virtualenv.

The command was: 

git fetch origin && git checkout release_18.09 && git pull --ff-only origin release_18.09

Cheers

ADD REPLY • link written 15 days ago by david.a.morais • 110

Then you used 

 $ sh run.sh

to start it up or something else?

ADD REPLY • link written 15 days ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

I usually start Galaxy using supervisord. Following your suggestion, I ran run.sh then upgraded the DB and everything is working fine now.

Thank you very much :)

ADD REPLY • link written 15 days ago by david.a.morais • 110

Wow, great news & glad it worked out!

ADD REPLY • link written 15 days ago by Jennifer Hillman Jackson ♦ 25k
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