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This commit is contained in:
Nicola Soranzo
2020-02-26 10:54:56 +01:00
committed by mvdbeek
parent 4c712f0f2d
commit 99bc25f4cc
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@@ -3,31 +3,40 @@
Galaxy's core functionality is currently supported on Python **2.7** (although
deprecated) and **>=3.5** .
If Galaxy complains about the version of Python you are using, check that
`python --version` reports a supported version. If this is not the case:
If Galaxy complains about the version of Python you are using:
1. Completely remove the virtualenv used by Galaxy, e.g. with:
`rm -rf /path/to/galaxy/.venv`
1. Completely remove the Python virtualenv used by Galaxy (which can be
configured with the `GALAXY_VIRTUAL_ENV` environment variable and defaults to
`.venv`), e.g. with: `rm -rf /path/to/galaxy/.venv`
2. Let Galaxy know the path of the correct version of Python.
2. If you were using a Python from a conda environment (which can be configured
with the `GALAXY_CONDA_ENV` environment variable and defaults to `_galaxy_`),
remove it, e.g. with: `conda env remove -n _galaxy_`
- If you are using Galaxy >= 20.05, just execute:
`export GALAXY_PYTHON=/path/to/python`
- If instead you are using an older version of Galaxy, you can manipulate
your shell's `$PATH` variable to place the correct version first. This can
be done for just Python by creating a new directory, adding a symbolic
link to python in there, and putting that directory at the front of
`$PATH`:
3. Let Galaxy know which Python to use in one of the following methods:
```sh
% mkdir ~/galaxy-python
% ln -s /path/to/python ~/galaxy-python/python
% export PATH=~/galaxy-python:$PATH
```
- If using Galaxy with a conda environment, remove conda environment (e.g. ```rm -rf /path/to/conda/__galaxy__```)
- If you want to use Python from conda, just activate the `base` environment
and Galaxy will create a new conda environment for itself.
- Otherwise:
1. Make sure a supported version of Python is installed.
2. Verify that the Python interpreter you want to use is first in the
output of `which -a python3 python` (or `which -a python` if you are
using Galaxy <=20.01). If this is not the case:
- If you are using Galaxy >= 20.05, just execute:
`export GALAXY_PYTHON=/path/to/python`
- If instead you are using an older version of Galaxy, you can
manipulate your shell's `PATH` variable to place the correct version
first. This can be done for just Python by creating a new directory,
adding a symbolic link to `python` in there, and putting that
directory at the front of `PATH`:
3. Start Galaxy again.
```sh
% mkdir ~/galaxy-python
% ln -s /path/to/python ~/galaxy-python/python
% export PATH=~/galaxy-python:$PATH
```
4. Start Galaxy again.
N.B. If you have compiled your own Python interpreter from source, please ensure
that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be