Re: [galaxy-dev] All Jobs Error Out

[Yip, Miu ki]

Hi John,

Thanks for the reply. I saw in the stack trace that there was a issue with 
mercurial, which was recently installed in the system. After uninstalling it, 
everything ran again. Not entirely sure what happened.

Thanks,
Miuki
On Mar 14, 2017, at 8:27 AM, John Chilton 
> wrote:

https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers

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Re: [galaxy-dev] All Jobs Error Out

[John Chilton]

Did you figure this out?

It looks like you jobs are not detecting Galaxy's virtualenv and so
they are getting a dependency (in this case mercurial) from Galaxy
root packages.

I'd review this document:
https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers

If you still have problems and that doesn't give you any ideas -
perhaps share your job_conf.xml.

-John


On Tue, Mar 7, 2017 at 5:14 PM, Yip, Miu ki  wrote:
> Hi all,
>
> This afternoon, our local instance of Galaxy suddenly started producing 
> errors for all jobs. This is the trace that gets printed out. Not sure what 
> is happening because the error doesn’t give much information other than 
> python not being able to find a module.
>
> Traceback (most recent call last):
>   File 
> "/localdata1/galaxy/database/jobs_directory/002/2931/set_metadata_LMpe2m.py", 
> line 1, in
> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
>   File "/localdata1/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, 
> in
> import galaxy.model.mapping  # need to load this before we unpickle, in 
> order to setup properties assigned by the mappers
>   File "/localdata1/galaxy/lib/galaxy/model/mapping.py", line 19, in
> from galaxy.model.custom_types import JSONType, MetadataType, 
> TrimmedString, UUIDType
>   File "/localdata1/galaxy/lib/galaxy/model/custom_types.py", line 13, in
> from galaxy import app
>   File "/localdata1/galaxy/lib/galaxy/app.py", line 17, in
> from galaxy.visualization.plugins.registry import VisualizationsRegistry
>   File "/localdata1/galaxy/lib/galaxy/visualization/plugins/registry.py", 
> line 15, in
> from galaxy.visualization.plugins import plugin as vis_plugins
>   File "/localdata1/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 
> 13, in
> from galaxy.web.base import interactive_environments
>   File "/localdata1/galaxy/lib/galaxy/web/base/interactive_environments.py", 
> line 14, in
> from galaxy.tools.deps.docker_util import DockerVolume
>   File "/localdata1/galaxy/lib/galaxy/tools/__init__.py", line 60, in
> import tool_shed.util.repository_util as repository_util
>   File "/localdata1/galaxy/lib/tool_shed/util/repository_util.py", line 16, in
> from tool_shed.util import hg_util
>   File "/localdata1/galaxy/lib/tool_shed/util/hg_util.py", line 11, in
> from mercurial.exchange import readbundle
>   File "/lib64/python2.7/site-packages/mercurial/exchange.py", line 18, in
> from . import (
>   File "/lib64/python2.7/site-packages/mercurial/bundle2.py", line 168, in
> urlerr = util.urlerr
> AttributeError: 'module' object has no attribute 'urlerr'
>
> Could anyone provide any insight on the issue? Thanks!
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