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#g...
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@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! ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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