Base Package Installation

Introduction

PerMedCoE project developments are based on containers enabling reproducible operations in heterogeneous HPC infrastructures, and their inclusion into building blocks (BBs) and workflows.

The permedcoe package provides a command line tool that eases BB execution. It also provides a Python API necessary for the development of BBs and enables the creation of empty BB templates.

This section shows how to install the PerMedCoE base package. A list of package dependencies is also provided.

Requirements

Python >= 3.6
Singularity (Apptainer)

Installation from Pypi

The package is publicly available in Pypi:

python3 -m pip install permedcoe

Installation from source code

An automatic installation script is available in the PerMedCoE base package GitHub repository:

git clone https://github.com/PerMedCoE/permedcoe.git
cd permedcoe
./install.sh

Attention

This script creates a file named installation_files.txt to keep track of the installed files. It is used with the uninstall.sh script to clean up the system.

Uninstall from Pypi

The base package can be uninstalled can be done using pip uninstall:

python3 -m pip uninstall permedcoe

Uninstall from source code

If installed using install.sh, the base package can be uninstalled by running:

./uninstall.sh

The folder can then be cleaned using the clean.sh script.

./clean.sh