inab / vre_progeny_executor

PROGENy tool job executor for iPC VRE

VRE PROGENy Tool Executor

Requirements

• Python 3.6 or later
• R 4.0.2 or later
• git

sudo apt update
sudo apt install python3
sudo apt install r-base
sudo apt install git

In order to install the Python dependencies you need pip and venv modules.

sudo apt install python3-pip python3-venv

Installation

Directly from GitHub:

cd $HOME
git clone https://github.com/inab/vre_progeny_executor.git
cd vre_progeny_executor

Create the Python environment:

python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip wheel
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

License

• © 2020-2022 Barcelona Supercomputing Center (BSC), ES
• © 2020-2022 Heidelberg University Hospital (UKL-HD), DE

Licensed under the Apache License Version 2.0, see the file LICENSE for details.