Installation

Required dependencies:

• Bash
• Python3
• Java

Recommended dependencies:

• Postgres

We recommend using a python3 virtual environment (or some equivalent like pyenv).

Installation:

git clone https://github.com/elip12/psl-gwas.git
cd psl-gwas
./bin/startproject.sh <project>

This will create a project directory with the given project name, copy all necessary files into it, and install all necessary python packages.

The project directory has the following structure:

<project>/
....gwas.psl            defines PSL model
....gwas.data           defines PSL data files
....parameters.yaml     optional, replaces some command-line params
....data/               holds data files
........raw/            holds raw data files
........preprocessed/   holds preprocessed data files
........postprocessed/  holds postprocessed data files