Installation

From PyPi

The PPP can also be easily installed via the PyPi repository via pip:

pip install py-popgen

From Conda

The PPP has conda packages available for python versions 3.6 and 3.7. To install in a clean environment, run the following:

conda create -n py-popgen python=3.7.7
conda activate py-popgen
conda install -c jaredgk -c bioconda py-popgen

From Source

The most current version of the PPP can be installed by obtaining the source code from the PPP GitHub repository. This can be done with:

git clone https://github.com/jaredgk/PPP

It can then be installed with either of these two commands, after CDing into the created directory (first allows editing the source code, second installs from source):

pip install -e .

python setup.py install

Dependencies

If installing PPP from source, multiple python and non-python depencencies must also be installed.

Python Dependencies

The PPP requries a number of python libraries, including:

• The SciPy Ecosystem (i.e. numpy, scipy, pandas, matplotlib, etc.)
• Pysam
• Biopython
• Cython
• rpy2

We recommend users install and maintain these libraries using either pip or Anaconda 3.

Other Dependencies

The PPP also requries a number of executables to be installed, including:

• VCFtools
• BCFtools, Samtools, and HTSlib
• plink 1.9
• plink 2.0
• SHAPEIT
• Beagle 5.0
• Picard

Please note that VCFtools, BCFtools, Samtools, HTSlib, plink 1.9, plink 2.0, and SHAPEIT may be installed using Anaconda 3.