.. _install:

Installing ProPhyle
===================


ProPhyle is written in Python, C and C++. It is distributed as a Python package
and all C/C++ programs are compiled upon the first execution
of the main program. ProPhyle requires a Unix operating system and the following dependencies:

* Python 3.3+ with the `ETE3 library <http://etetoolkit.org/>`_
* GCC 4.8+
* ZLib

There are multiple ways of installation:

.. contents::
	:depth: 1
	:local:
	:backlinks: none


Installing ProPhyle using Bioconda
----------------------------------

To set-up Bioconda, install
`Miniconda <https://conda.io/miniconda.html>`_
or another Conda distribution, and
add `Bioconda channels <https://bioconda.github.io/>`_

.. code-block:: bash

	conda config --add channels defaults
	conda config --add channels conda-forge
	conda config --add channels bioconda

You may either create a separate Conda environment
(which is the recommended approach)

.. code-block:: bash

	conda create -n prophyle prophyle
	source activate prophyle

or install ProPhyle directly to your main environment

.. code-block:: bash

	conda install prophyle


Installing ProPhyle using PIP
-----------------------------

There are three options of installing ProPhyle using PIP.

1) From PyPI

	.. code-block:: bash

		pip install -U prophyle

2) From Git

	.. code-block:: bash
	
		pip install -U git+https://github.com/prophyle/prophyle

3) From PyPI to the current directory

	.. code-block:: bash

		pip install --user prophyle
		export PYTHONUSERBASE=`pwd`
		export PATH=$PATH:`pwd`/bin



Running ProPhyle directly from the repository
---------------------------------------------

It also is possible to run ProPhyle directly from the repository, by calling
the main script

.. code-block:: bash

	prophyle/prophyle/prophyle.py

or its alias

.. code-block:: bash

	prophyle/prophyle/prophyle

ProPhyle will then automatically adjust all paths of the auxiliary programs.

Note that ProPhyle uses submodules, therefore the repository needs to
be clonned with the `--recursive` option

.. code-block:: bash

    git clone --recursive http://github.com/prophyle/prophyle


Adjusting the PATH variable
~~~~~~~~~~~~~~~~~~~~~~~~~~~

The ProPhyle path can be prepended to the `$PATH` variable so that ProPhyle
can be executed in the same way as if it was installed using PIP

.. code-block:: bash

    export PATH=$(pwd)/prophyle/prophyle:$PATH


Installing dependencies
~~~~~~~~~~~~~~~~~~~~~~~

When run from the repository,
some of the ProPhyle dependencies, listed in `requirements.txt`, might
be missing in the system.
It is possible to install them either using BioConda

.. code-block:: bash

    cat prophyle/requirements.txt | perl -pe 's/==.*//g' | xargs conda install

or using PIP

.. code-block:: bash

    cat prophyle/requirements.txt | xargs pip install