Installation

pip

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.

$ python -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://github.com/galaxyproject/planemo.git

If your PATH contains a Python installed through Conda it should likely not be used to run Planemo, please consider using a tool such uv to manage native Python installations and environments.

Planemo runs on Python 3.8 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.

uv

uv is a modern Python package manager that can be used to install Planemo. Information on installing uv can be found at https://docs.astral.sh/uv/getting-started/installation/. Once uv has been installed and its environment sourced in your shell, you can install Planemo using the following commands:

$ uv tool install planemo

Installing Planemo as a tool will setup a global shim that manages the Python environment used for Planemo without having to manage this yourself like the pip method described above. The Planemo executable planemo will just be on your path whenever the uv environment is active.

uv can also be used to upgrade Planemo to the latest version with the following command:

$ uv tool upgrade planemo

rye

rye is another modern Python package manager. Information on installing rye can be found at https://rye.astral.sh/guide/installation/. Once rye has been installed and its environment sourced in your shell, you can install Planemo using the following commands:

$ rye tools install planemo

Installing Planemo as a tool will setup a global shim that manages the Python environment used for Planemo without having to manage this yourself like the pip method described above. The Planemo executable planemo will just be on your path whenever the rye environment is active.

Note

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.