Question: After update my Galaxy won't start - ImportError: No module named error_level
0
gravatar for 47760468
4.0 years ago by
4776046810
China
4776046810 wrote:

After update my galaxy,there is an error,as blow:

root@kick-virtual-machine:~/galaxy-dist# sh run.sh
Traceback (most recent call last):
 
  File "/root/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module>
    from galaxy import config, jobs, util, tools
  File "/root/galaxy-dist/lib/galaxy/tools/__init__.py", line 38, in <module>
    from galaxy.jobs.error_level import StdioErrorLevel
ImportError: No module named error_level

 

 

upgrade local startup errors • 2.1k views
ADD COMMENTlink modified 4.0 years ago by Martin Čech ♦♦ 4.9k • written 4.0 years ago by 4776046810
1

Did you make any modifications to your Galaxy? (i.e. what does `hg status` say?)

Does your folder contain  lib/galaxy/jobs/error_level.py ?

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Martin Čech ♦♦ 4.9k

Thank you for answering.I just check my galaxy folder ,there is not a file named error_level.py.When I print hg incoming ,it show no changes found.

ADD REPLYlink written 4.0 years ago by 4776046810

What does  `hg status` say?

ADD REPLYlink written 4.0 years ago by Martin Čech ♦♦ 4.9k

There are too many sentences,I only can list a part of them:

? lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
? lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
? lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py

..... (shortened by moderator)

 

ADD REPLYlink modified 4.0 years ago by Martin Čech ♦♦ 4.9k • written 4.0 years ago by 4776046810

I see the wiki about updata galaxy,use the "hg pull -u".

ADD REPLYlink written 4.0 years ago by 4776046810

Thank you for replying.

However,after I execute 'hg update --clean',and then restart my galaxy ,there is still a error.

Traceback (most recent call last):

  File "/root/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module>
    from galaxy import config, jobs, util, tools
  File "/root/galaxy-dist/lib/galaxy/tools/__init__.py", line 38, in <module>
    from galaxy.jobs.error_level import StdioErrorLevel
ImportError: No module named error_level

ADD REPLYlink modified 4.0 years ago by Martin Čech ♦♦ 4.9k • written 4.0 years ago by 4776046810

what does the following command say?

hg paths
ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Martin Čech ♦♦ 4.9k

default = https://bitbucket.org/galaxy/galaxy-dist/

 

ADD REPLYlink written 4.0 years ago by 4776046810
1
gravatar for Martin Čech
4.0 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

It looks like your Galaxy did not update properly, the files with `?` in front of them are not being tracked by the mercurial.

How exactly did you try to update your Galaxy?

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Martin Čech ♦♦ 4.9k
1
gravatar for Dannon Baker
4.0 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

It does sound like your update didn't complete correctly.  If you don't have any local changes to the codebase (functionality you've added), then you might be able to simply execute 'hg update --clean' to get back to a working copy.

ADD COMMENTlink written 4.0 years ago by Dannon Baker3.7k
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