galaxy/doc/source/admin/python.md

Supported Python versions

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:

1. Completely remove the virtualenv used by Galaxy, e.g. with: rm -rf /path/to/galaxy/.venv

2. Let Galaxy know the path of the correct version of Python.

   • 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:

     % 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__)

3. 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 imported after installation. These "extra" modules are built at the end of the compilation process and are required by the Galaxy framework. If building on Linux, you may need to install the appropriate -dev packages for OpenSSL and Bzip2. You may also need to build Python with shared libraries (--enable-shared).