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Installation

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

P4 needs Python 3; it no longer works with Python 2.

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.

Preparations for the full install on the Mac

You probably want to install Homebrew and install Python3 from there. 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. If that does not work, you may be able to install them via:

xcode-select --install

You don't need the full Xcode for this (but if you want it, it is available from the Apple App Store).

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

You can install scipy with pip3; it will install numpy as well. You will also need bitarray.

Preparations for the full install on Ubuntu Linux

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 16.04, 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.

Installing by getting dependencies using conda

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.

Installing it in-place

The usual way that Python packages are installed uses setup.py to installs 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.

Updating from git

The motivation for installing it in-place is that it makes it easy to update. Generally all you need to do is to go to the p4 git directory and say:

git pull

That is usually sufficient.

Occasionally there may have been changes to the C-language code in the pf module. If that is the case (would you be able to see those files as they are updated?), and you use the pf module then you would need to do:

python3 setup.py build_ext -i

You would also need to do that when you install it in-place for the first time, or if you make any changes to the C-language code yourself. If you are not sure rebuilding is needed, it's OK to do it anyway.

Installing scqdist and pytqdist

You will need one of these if you do tree-to-tree quartet distances. See the directories Qdist and tqDist in the source, with their own instructions.

To see if it works

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.)

Deinstallation

There is a func.uninstall() function, which may work. You may need to run it as root, or use sudo.

If that does not work, then recall that things get installed in 3 places. Search out the Python package, the p4 script, and the examples.

If you want to statically link your gsl libs

For those who may not want to do the usual dynamic linking of gsl libs, it is possible to statically link the gsl libs to the pf.so module when you build it. See the setup.py file, and uncomment and adjust the extra_link_args line.