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:
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 <myip(a)cshl.edu> 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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