I have a new (fresh) install of the Galaxy 16.07 (change_set 727270261750fc71979e7ba9fec96b10091ff104). I am having problems to upload files to this Galaxy. In the logs the error appears as
Traceback (most recent call last): File "/srv/galaxy/database/job-working-directory/000/5/set_metadata_OIPLOE.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/srv/galaxy/server/lib/galaxy_ext/metadata/set_metadata.py", line 23, in <module> from sqlalchemy.orm import clear_mappers ImportError: No module named sqlalchemy.orm
While in the sdterr the error shown is
Traceback (most recent call last): File "/srv/galaxy/server/tools/data_source/upload.py", line 17, in <module> from six.moves.urllib.request import urlopen ImportError: No module named six.moves.urllib.request
I used the galaxy ansible playbook to install. The installation includes the python virtualenv (2.7.12) and I have conda installed in tool-dependency/_conda ( the whole path less the 50 chars!).
All the installation was fine and the tool installation also went as expected (I also use dependency_resolvers.xml). Inside my galaxy.ini the conda is enabled with the options:
conda_ensure_channels = conda-forge,r,bioconda,iuc conda_auto_install = True conda_auto_init = True
I also set in my job_config.xml
<destinations> <destination id="local" runner="local"> <param id="embed_metadata_in_job">False</param> <env file="/srv/galaxy/server/.venv/bin/activate" /> </destination> </destinations>
Without "embed_metadata_in_job" the UCSC get data fails. And I set the "env file" in a hope that python would not have problems to find its packages (as described in the galaxy website).
Right now all the jobs are local and since this is still a test a have no handler running. I am using postgres + ngnix (all playbooks installed). All tools have been installed using Enis playbook as well (which worked amazingly well).
Finally, when I first run the upload tool (upload local file) I can see conda fetching and installing all dependencies, but the job still fails.
Can you please help me to figure out why upload is not working?
BTW, the other tools are working, despite the fact that the " ImportError: No module named sqlalchemy.orm" error is still showing in the the logs.