VRE Executor template

Example pipelines file integrating ProGeny. It is ready to run in the VRE matching the code in the HowTo documentation.

This repo structure fits well any R-based tool and might be used as the base template for future tools. It should have all of the base functionality and is set up for unit testing and with pylint to ensure code clarity.

Requirements

• Python 3.6 or later (Recommended 3.7)
• Python3.6-pip, Python3.6-dev and Python3.6-venv or later
• R-4.0
• R library to be integrated: PROGENy

Install python enviroment and R:

sudo apt update
sudo apt install python3.6 
sudo apt install python3.6-pip python3.6-dev python3.6-venv
sudo apt install r-base

Install the particular R library and its dependencies:

sudo su
su www-data -s /bin/bash
./Rprogeny.sh
su user

Installation

Directly from GitHub:

cd $HOME
git clone $THIS_REPO

Create the Python environment:

python3 -m venv $HOME/$THIS_REPO/venv
source venv/bin/activate
pip install -r requirements.txt

Run the Wrapper

./VRE_RUNNER --config tests/basic/config.json --in_metadata tests/basic/in_metadata.json --out_metadata out_metadata.json --log_file VRE_RUNNER.log