Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities

TL;DR

This paper reviews current methods for packaging, virtualization, and containerization of omics software, discussing their benefits, challenges, and proposing principles to enhance reproducibility and sustainability in biomedical research.

Contribution

It provides a systematic review of platforms and practices, highlighting challenges and proposing principles for sustainable, reproducible omics software deployment.

Findings

Analyzes advantages and limitations of each approach

Identifies key challenges in omics software packaging

Proposes principles for sustainable and reproducible practices

Abstract

Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging, virtualization, and containerization are different approaches to satisfy this need by wrapping omics tools in additional software that makes the omics tools easier to install and use. Here, we systematically review practices across prominent packaging, virtualization, and containerization platforms. We outline the challenges, advantages, and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers, and system administrators. We also propose principles to make packaging, virtualization, and containerization of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.