[SOLVED] galaxy.model.migrate.check can't manage conda virtual env

Question: [SOLVED] galaxy.model.migrate.check can't manage conda virtual env

20 days ago by

Hi,

I'm pretty new to galaxy configuration and I have a error that I can't handle. I've installed galaxy with a hand made conda virtual env. Galaxy is in a directory of galaxy user system /home/galaxy/galaxy/. I have change the conda_prefix in config/galaxy.yml :

conda_prefix : /opt/anaconda3/

and there is this env variable :

~/galaxy$ echo $GALAXY_VIRTUAL_ENV
/home/galaxy/.conda/envs/galaxy

I use a postgresql database and when I start the app I have this error :

galaxy@anesidora:~/galaxy$ conda activate galaxy
(galaxy) galaxy@anesidora:~/galaxy$ uwsgi --yaml config/galaxy.yml
[uWSGI] getting YAML configuration from config/galaxy.yml
[......]   
 galaxy.model.migrate.check INFO 2018-11-08 16:07:20,795 [p:18996,w:0,m:0] [MainThread] At database version 141
    Traceback (most recent call last):
      File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
        app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
      File "lib/galaxy/app.py", line 84, in __init__
        self._configure_models(check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file)
      File "lib/galaxy/config.py", line 1132, in _configure_models
        verify_tools(self, install_db_url, config_file, install_database_options)
      File "lib/tool_shed/galaxy_install/migrate/check.py", line 65, in verify_tools
        raise Exception("Error attempting to update the value of migrate_tools.version: %s" % output)
    Exception: Error attempting to update the value of migrate_tools.version: Activating virtualenv at /home/galaxy/.conda/envs/galaxy
    manage_db.sh: 100: .: Can't open /home/galaxy/.conda/envs/galaxy/bin/activate

I guess that the app try to manage conda virtual envs like python virtualenv but I don't know what to do next...

Note that I have a successful run just before when galaxy does not try to "check".

Thank's for any help.

arnome.

software error • 69 views

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modified 17 days ago • written 20 days ago by arnaud.mounier • 10

19 days ago by

arnaud.mounier • 10

arnaud.mounier • 10 wrote:

Hi, gitter discussion solve the issue. It's best to create a virtualenv within conda not with a conda virtual enviroment :

conda create --yes --name _galaxy_ 'python=2.7' 'pip>=9' 'virtualenv=16' -c 'conda-forge'
source activate _galaxy_
virtualenv .venv

Thanks to Marius van den Beek @mvdbeek. arnome.

ADD COMMENT • link written 19 days ago by arnaud.mounier • 10

20 days ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It doesn't look like you fully configured to force Galaxy to not use vitrualenv and use conda instead.

To start with, please see the help here: https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#conda

If you run into more problems, please write to the developers for advice at our Gitter channel. The 18.09 release is new, running Galaxy under conda is a more difficult approach, and there might be some technical/corner case undiscovered issue in the framework code. They'll be able to help troubleshoot for all: https://gitter.im/galaxyproject/Lobby (better, if you have a GitHub account) or https://galaxyproject.org/ > "Open chat" (anyone).

Thanks! Jen, Galaxy team

ADD COMMENT • link written 20 days ago by Jennifer Hillman Jackson ♦ 25k

20 days ago by

arnaud.mounier • 10

arnaud.mounier • 10 wrote:

Hello,

thank's for the reply. The problem is that I don't see what I miss. I redefined a virtual env with conda specifically for 18.09 version (there is one missing package in requirements.txt : psycopg2-binary) called galaxy.1809. If I launch galaxy via uwsgi with :

the sqlite version : it works ;
the postgresql data base setup : the same error occur.

Thanks ! arnome.

ADD COMMENT • link written 20 days ago by arnaud.mounier • 10

Gitter discussion starts here: https://gitter.im/galaxyproject/Lobby?at=5be59358e8add80e63c7088a

ADD REPLY • link written 19 days ago by Jennifer Hillman Jackson ♦ 25k

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