Use virtualenv when conda is on PATH #6975
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The selenium errror looks very much unrelated. |
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| Versions of Galaxy prior to 18.05 could install in to the base/root Conda environment. Consult the correct version | ||
| of the documentation for your version of Galaxy. |
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Should we keep this warning?
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Not sure if this would clarify or make things more confusing? I could add a warning to the top that this applies to 19.01 or newer, for older version consult the documentation for your version of Galaxy ?
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Yeah, that seems reasonable.
This uses our proper pinned requirements and is sginificantly easier to set up and maintain.
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@mvdbeek Yep, I understand the conda/venv weirdness now -- that was an interesting dive |
| 100% |████████████████████████████████| 2.2MB 66.1MB/s | ||
| Installing collected packages: bx-python | ||
| Successfully installed bx-python-0.7.3 | ||
| A Conda environemnt named ``_galaxy_`` will be created using python 2 and the appropriate virtualenv package will be installed into this environment. |
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s/environemnt/environment
| Installing collected packages: bx-python | ||
| Successfully installed bx-python-0.7.3 | ||
| A Conda environemnt named ``_galaxy_`` will be created using python 2 and the appropriate virtualenv package will be installed into this environment. | ||
| Using this environemnt a ``.venv`` is initialized. This is a one-time setup, and all other activation and dependency |
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s/environemnt/environment
| if [ "$CONDA_DEFAULT_ENV" != "$GALAXY_CONDA_ENV" ]; then | ||
| if ! check_conda_env "$GALAXY_CONDA_ENV"; then | ||
| echo "Creating Conda environment for Galaxy: $GALAXY_CONDA_ENV" | ||
| echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_CONDA_ENV to an" | ||
| echo "existing environment before starting Galaxy." | ||
| $CONDA_EXE create --yes --name "$GALAXY_CONDA_ENV" 'python=2.7' 'pip>=9' | ||
| $CONDA_EXE create --yes --name "$GALAXY_CONDA_ENV" 'python=2.7' 'pip>=9' 'virtualenv=16' -c 'conda-forge' |
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@mvdbeek Is there any specific reason to pin virtualenv to 16 or can this be relaxed to >=16 ?
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No specific reason, >=16 is fine.
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Cool, I'll adding to the PR I'm working on, thanks!
- Use `conda_activate`, which works also under dash - Run `conda_activate` also when `$GALAXY_CONDA_ENV` already exists - Run `virtualenv` when the conda env is active but `$GALAXY_VIRTUAL_ENV` does not exist - Update the default for `GALAXY_CONDA_ENV` in scripts/common_startup_functions.sh Follow-up on galaxyproject#6975 .
This uses our proper pinned requirements and is significantly easier to set up and maintain.
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