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    Björn Grüning
    @bgruening
    here the issue: unbit/uwsgi#1978
    and if I get this correct, we are bound to python 3.6
    I just wrote an email to all people with .it in their mail address ;)
    Pablo Moreno
    @pcm32

    I’m suddenly getting this error when trying to execute tools on my planemo setups with galaxy-19.05 and galaxy-20.01, both with planemo 0.70 and older planemos…

    galaxy.jobs.handler INFO 2020-05-28 10:51:36,182 (2) Job dispatched
    Traceback (most recent call last):
      File "/Users/pmoreno/miniconda3/bin/conda", line 12, in <module>
        from conda.cli import main
    ModuleNotFoundError: No module named ‘conda’

    I tried installing pip install conda on the .venv without success to fix this… have you come across this?

    with python 2.7 and python3
    Pablo Moreno
    @pcm32
    This happens both starting in conda deactivated shell or on an activated one (I would normally do conda deactivate and then source ~/venvs/planemo/bin/activate and then planemo serve…)
    conda on its own works well and I haven’t done any change there….
    Nicola Soranzo
    @nsoranzo
    @pcm32 macOS?
    Pablo Moreno
    @pcm32
    yes
    I have now removed ~/.planemo, removed the venv, recreated the venv (virtualenv py3), installed planemo, going to delete the galaxy venv in question and re-create just to be sure.
    Marius van den Beek
    @mvdbeek
    You always need to use the same interpreter when you use planemo. If you switch you need to remove ~./planemo/gx-venv
    Pablo Moreno
    @pcm32
    I am using a galaxy root and the .venv inside it, to avoid using gx-venv, this should be fine, right?
    Marius van den Beek
    @mvdbeek
    If your interpreters line up, yes
    But that can be tricky to get right
    Pablo Moreno
    @pcm32
    yes, agreed…
    I’m using python3 from brew, there are no objections to that in general, correct? provided it is always the same, right?
    Pablo Moreno
    @pcm32
    …dammed… still No module named ‘conda’…..
    Nicola Soranzo
    @nsoranzo
    @pcm32 I'm pretty positive the issue is with virtualenv, what does virtualenv --version print for you?
    Pablo Moreno
    @pcm32
    yes, I’m redoing everything with python3 -m venv … now...
    Nicola Soranzo
    @nsoranzo
    That's not going to help actually
    Pablo Moreno
    @pcm32
    Re virtualenv:
    virtualenv --version
    virtualenv 20.0.20 from /usr/local/lib/python3.6/site-packages/virtualenv/__init__.py
    Nicola Soranzo
    @nsoranzo
    Mmh, that should work
    Pablo Moreno
    @pcm32
    funny is that when I execute that virtualenv, it places the brew python inside the env created.
    whereas is I do python3 -m venv it places the /usr/local/bin/python3 which is not brews...
    Nicola Soranzo
    @nsoranzo
    You can specify which one to use with virtualenv -p /path/to/python
    Pablo Moreno
    @pcm32
    …mmm… no, no difference either… still No module named conda on tool execution...
    let me try using planemos gxa_venv instead of Galaxy’s (which I have deleted and re-recreated on every iteration, but still…)
    …mmm, so planemo goes with python2.7 by default in its gx_venv….
    Nicola Soranzo
    @nsoranzo
    This is the issue I reported, which seems the same and was fixed in virtualenv 20.0.14: pypa/virtualenv#1704
    Pablo Moreno
    @pcm32
    yes, seems to be the same issue...
    I also noted that when I used virtualenv it would say something about CPython, whereas as using the module makes no mention of it. I used initially virtualenv as I understand is a better solution that using the module naked...
    …mmm… same issue from planemo gx_venv...
    Nicola Soranzo
    @nsoranzo
    The workaround to fix the venv issue is implemented only inside virtualenv (and in Python >3.8.2)
    Pablo Moreno
    @pcm32
    so I need to upgrade python then. Which python flavour do you use for Galaxy @nsoranzo ? brew? I understand that Galaxy used not to like to run on conda based python, is that still the case?
    Nicola Soranzo
    @nsoranzo
    I use Linux, so no such issues!
    Pablo Moreno
    @pcm32
    hahaha, ok
    Nicola Soranzo
    @nsoranzo
    Anyway conda Python has been fine for years
    but still together with virtualenv
    Pablo Moreno
    @pcm32
    …mm.. not the last time I tried around a year… let see...
    Pablo Moreno
    @pcm32
    ok, with python 3.8.2 (used pyenv to avoid disrupting my conda world) it works, uff...
    thanks @nsoranzo
    Marius van den Beek
    @mvdbeek
    looks like quay.io is down right now, that breaks container resolution :/
    Nicola Soranzo
    @nsoranzo
    Second time in 10 days...
    Pablo Moreno
    @pcm32
    are we able to point galaxy to a different docker registry? I heard once from @bgruening that all biocontainer images were mirrored at an EBI docker registry… is that so?
    Marius van den Beek
    @mvdbeek
    yes, you just need to change the namespace of the resolver
    Pablo Moreno
    @pcm32
    in the containers resolver conf file?
    Marius van den Beek
    @mvdbeek
    yes
    Pablo Moreno
    @pcm32
    ok, we only need to find out if such a replacement registry does exist or not...
    Marius van den Beek
    @mvdbeek
    it may not work out of the box, but the code doesn’t hardcode quay.io
    I think all you need to do is set the namespace attribute in the mulled / cached_mulled / build_mulled resolvers