3. 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:

There are multiple ways of installation:

3.1. Installing ProPhyle using Bioconda

To set-up Bioconda, install Miniconda or another Conda distribution, and add Bioconda channels

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)

conda create -n prophyle prophyle
source activate prophyle

or install ProPhyle directly to your main environment

conda install prophyle

3.2. Installing ProPhyle using PIP

There are three options of installing ProPhyle using PIP.

  1. From PyPI

    pip install -U prophyle
  2. From Git

    pip install -U git+https://github.com/prophyle/prophyle
  3. From PyPI to the current directory

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

3.3. Running ProPhyle directly from the repository

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


or its alias


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

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

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

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

or using PIP

cat prophyle/requirements.txt | xargs pip install