Question: Fail to upload data to local Galaxy 16.07
gravatar for david.a.morais
3 months ago by
david.a.morais110 wrote:


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/", line 1, in <module>
    from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
  File "/srv/galaxy/server/lib/galaxy_ext/metadata/", 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/", 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

       <destination id="local" runner="local">
         <param id="embed_metadata_in_job">False</param>
         <env file="/srv/galaxy/server/.venv/bin/activate" />

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.


ADD COMMENTlink modified 6 days ago by heidi.hough0 • written 3 months ago by david.a.morais110
gravatar for david.a.morais
3 months ago by
david.a.morais110 wrote:


After talking to Bjoern Gruening, he found the solution to fix the upload problem.

  1. Install samtools 0.1.19
  2. Create a symlink inside tool-dependency pointing to the installation dir

    ln -s /tool-dependency/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/ /tool-dependency/samtools/default/

This solved the problem of the uploading tool.

Big thanks to Bjoern for that.

ADD COMMENTlink written 3 months ago by david.a.morais110

Where did you find out where samtools was installed?

ADD REPLYlink written 19 days ago by veidar450

It should be inside your /tool-dependency/ directory (after you have it installed via toolshed)

Somewhere like


ADD REPLYlink written 12 days ago by david.a.morais110
gravatar for heidi.hough
6 days ago by
heidi.hough0 wrote:

I'm encountering a similar issue, but creating the link does not resolve my problem. What else should I be looking for? Also, running v17.01 rather than 16.07 as the OP


I recreated the .vdev and restarted and it's working.

ADD COMMENTlink modified 6 days ago • written 6 days ago by heidi.hough0
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