For a traditional Python 2 installation of Planemo, first set up a virtualenv
planemo (this example creates a new one in
.venv) and then
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
use the following
pip install idiom instead:
$ pip install -U git+git://github.com/galaxyproject/planemo.git
PATH contains a Python installed through Conda it should likely not be used to run Planemo,
consider using the
-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 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.