This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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:

  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. 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_

  3. Let Galaxy know which Python to use in one of the following methods:

    • 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 <=19.09). If this is not the case:

        • If you are using Galaxy >= 20.01, 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
  4. Remove compiled mako templates when upgrading from Python 2:

    % rm -rf /path/to/galaxy/database/compiled_templates/

    These templated will be regenerated automatically when starting Galaxy.

  5. 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).