Getting ETE3 Running on a Mac

Unfortunately, ETE, Python framework for the analysis and visualization of (phylogenetic) trees, is not currently available to install through MacPorts. The recommended way to install ETE on a Mac is through Anaconda or a Miniconda setup. I confess I was not familiar with the conda open source package management system, and I had not heard of Miniconda. I like Anaconda quite a lot, and I like it even more now that I know it’s part of a larger open source ecosystem, and it may be that one day I will switch over to it, but, right now, I am fairly happy with my Macports setup and I would rather not break what’s working.

To get a better sense of what I need to do, I clicked on the Linux native installation directions, which skip conda:

Install dependencies: python-qt4, python-lxml, python-six and python-numpy

Those don’t look too bad. Python Six, a compatibility library for Python 2 and 3, is available as py34-six. Done. As for the rest: py34-pyqt4, py34-lxml, and, of course, py34-numpy are already installed. Done, again.

It looks like pip will work here, so after making sure I have py34-pip installed and making sure I run sudo port --select pip pip34 to set it, I can run:

sudo pip install ete3

If I run an IDLE session and import ete3, I get no error prompts. Yay! Time to make some spam.

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