For a traditional Python 2 installation of Planemo, first set up a virtualenv for planemo (this example creates a new one in .venv) and then install with pip. Planemo requires pip 7.0 or newer.

$ virtualenv .venv; . .venv/bin/activate
$ pip install "pip>=7" # Upgrade pip if needed.
$ pip install planemo

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

$ . .venv/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 in theory runs under Python 3 but Galaxy does not, so it is best to use a Python 2 with Planemo for now.

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 conda-forge
$ conda config --add channels bioconda
$ 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.