The PPP can also be easily installed via the PyPi repository via pip:
pip install py-popgen
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
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
To install the local repository copy and allow edits to the source code to be included with imports without any additional steps, run the following commands:
cd PPP pip install -e .
To install the repository without pip, run the following (note that any modifications to the source code will not be used at runtime unless the setup command is run again):
cd PPP python setup.py install
If installing PPP from source, multiple python and non-python depencencies must also be installed.
The PPP requries a number of python libraries, including:
The PPP also requries a number of executables to be installed, including:
Please note that VCFtools, BCFtools, Samtools, HTSlib, plink 1.9, plink 2.0, and SHAPEIT may be installed using Anaconda 3.