P4 — Installation

The source code is hosted at https://github.com/pgfoster/p4-phylogenetics

I’ve installed it on Linux and Mac OS X. In either case, you need to have the basic C-language programming tools, including a compiler, libraries, headers, and so on.

On a mac, you probably want to install and use Homebrew.

The command-line tools for development need to be installed for Homebrew to work, but the last time I installed Homebrew on my mac it did the installation of those command-line tools itself.

You can install a Python3 using homebrew. As explained here, in the section on PEP 668, you will want to put your Python3 in a virtualenv. You can install scipy with pip3; it will install numpy as well. From pip3 you will also need bitarray, biopython, setuptools, and you will probably want ipython for interactive use.

You will need the gsl library (Gnu Scientific Library), and the nlopt library. For this, Homebrew recommended.

If the installation process complains about lack of Python.h, then you need what on Ubuntu would be called python-dev.

I have recently installed p4 on Ubuntu 20.04, and had to

sudo apt-get install libgsl-dev
sudo apt-get install libnlopt-dev
sudo apt-get install python3-dev

You can use pip3 to install scipy (which gives you numpy) and bitarray.

And if you want to use the GUI tree-drawing

sudo apt-get install python-tk

Presumably other Ubuntu versions will be similar or identical.

This works without sudo. I recently installed p4 on a redhat cluster with help from conda (actually miniconda). To get the dependencies I did

conda install scipy gsl nlopt bitarray

Then I added the conda include and lib paths to the p4 setup.py file in lists my_include_dirs and my_lib_dirs.

The usual way that Python packages are installed uses setup.py to install the package in a separate location, but I don’t recommend it in this case, because I am too slow in making releases. It would be easier to install p4 in-place as described here. I have removed the source tarballs from the git repo to underline this. The advantage is that it makes it easier to keep up with the changes made to the git repo.

The first thing would be to clone it from GitHub. After that, you need to make it usable. Making it usable is needed on first installation, and not needed subsequently.

To make it usable in-place, you need to do three things, which in overview are

1. Add the p4 git directory, eg /usr/local/src/P4Git to your PYTHONPATH
2. Add the p4 git bin directory, eg /usr/local/src/P4Git/bin to your PATH
3. Build the pf module, installing it in-place

Now look at those three steps in detail. For example if you install it in your home directory, to add the p4 git directory to your PYTHONPATH, you might add something like the following line to your ~/.profile or ~/.bash_profile

export PYTHONPATH=$HOME/src/P4Git

(depending on where your P4 lib directory is, and what it is called), or you can add

export PYTHONPATH=$PYTHONPATH:$HOME/src/P4Git

if you already have a PYTHONPATH defined.

The second thing you will want to do is to add the location of the p4 script to your PATH. Similar to adjusting the PYTHONPATH above, you can add a line like this to your ~/.profile or ~/.bash_profile

export PATH=$PATH:$HOME/src/P4Git/bin

depending on where your P4 git directory is, and what it is called.

To build the pf module, say

python3 setup.py build_ext -i

It might actually work. If it doesn’t, note the error messages that flew by. The earliest error message is usually a clue.

git pull

python3 setup.py build_ext -i

If, in your shell, you are still in the same directory that you built it from, go to some other directory, or the following test will not work. Even better, use a new shell.

To see if you can load the package, start up python3 and then

import p4

To see if the p4 script works, say (perhaps from a new terminal) to your shell (not in interactive python)

p4 --help

(Once it gets installed, if everything went perfectly and it still does not work, try it in a new shell, or maybe even restart your terminal program to refresh your PATH and PYTHONPATH.)