For a traditional Python installation of Planemo, first set up a virtual environment for planemo (this example creates a new one in planemo) and then install with pip. Planemo requires pip 7.0 or newer.

$ python3 -m venv planemo
$ . planemo/bin/activate
$ pip install planemo

When installed this way, planemo can be upgraded as follows:

$ . planemo/bin/activate
$ pip install -U planemo

To install or update to the latest development branch of planemo with pip, use the following pip install idiom instead:

$ pip install -U git+git://

If your PATH contains a Python installed through Conda it should likely not be used to run Planemo, consider using the virtualenv argument -p to point at a non-Conda Python 2 executable installed natively on your system or using a tool such pyenv. virtualenv can be installed via Conda, pyenv, or a package manager - it should make no difference.

Planemo runs on Python 3.7 or newer. Planemo can be used to run multiple versions of Galaxy, but please note that the last Galaxy release that fully supports Python 2.7 is 19.09.

Conda (Experimental)

Another approach for installing Planemo is to use Conda (most easily obtained via the Miniconda Python distribution). Afterwards run the following commands.

$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda install planemo

Galaxy is known to have issues when running with a Conda Python so this approach should be considered experimental for now. If you have problems with it or hacks to make it work better - please report them.


The options --docker and --biocontainers for planemo serve and planemo test require that docker is installed on the system and that it can be run without root privileges. See Docker installation and run Docker without root privileges for further instructions.