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Approaches for containerized scientific workflows in cloud environments with applications in life science

Authors :
Spjuth, Ola
Capuccini, Marco
Carone, Matteo
Larsson, Anders
Schaal, Wesley
Novella, Jon Ander
Stein, Oliver
Ekmefjord, Morgan
Tommaso, Paolo Di
Floden, Evan
Notredame, Cedric
Moreno, Pablo
Hellander, Andreas
Emami Khoonsari, Payam
Herman, Stephanie
Kultima, Kim
Lampa, Samuel
Spjuth, Ola
Capuccini, Marco
Carone, Matteo
Larsson, Anders
Schaal, Wesley
Novella, Jon Ander
Stein, Oliver
Ekmefjord, Morgan
Tommaso, Paolo Di
Floden, Evan
Notredame, Cedric
Moreno, Pablo
Hellander, Andreas
Emami Khoonsari, Payam
Herman, Stephanie
Kultima, Kim
Lampa, Samuel
Publication Year :
2021

Abstract

Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses. In this article, we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm, Argo, Kubeflow, Luigi and SciPipe, when deployed in cloud environments. A particular focus is placed on the workflow tool’s interaction with the Kubernetes container orchestration framework.

Details

Database :
OAIster
Notes :
English
Publication Type :
Electronic Resource
Accession number :
edsoai.on1349083887
Document Type :
Electronic Resource
Full Text :
https://doi.org/10.12688.f1000research.53698.1