  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.
