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

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 513
Author(s):  
Ola Spjuth ◽  
Marco Capuccini ◽  
Matteo Carone ◽  
Anders Larsson ◽  
Wesley Schaal ◽  
...  
Keyword(s):  
Data Analysis ◽  
Life Science ◽  
Science Research ◽  
End Users ◽  
Scientific Workflows ◽  
Life Science Research ◽  
Cloud Environments ◽  
Container Orchestration

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.

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

2018 ◽  
Author(s):  
Ola Spjuth ◽  
Marco Capuccini ◽  
Matteo Carone ◽  
Anders Larsson ◽  
Wesley Schaal ◽  
...  
Keyword(s):  
Data Analysis ◽  
Life Science ◽  
Science Research ◽  
End Users ◽  
Scientific Workflows ◽  
Life Science Research ◽  
Cloud Environments ◽  
Container Orchestration

Containers are gaining popularity in life science research as they encompass all dependencies of provisioned tools and simplifies software installations for end users, as well as offering a form of isolation between processes. Scientific workflows are ideal to chain containers into data analysis pipelines to sustain reproducible science. In this manuscript we review the different approaches to use containers inside the workflow tools Nextflow, Galaxy, Pachyderm, 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.

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

2018 ◽  
Author(s):  
Ola Spjuth ◽  
Marco Capuccini ◽  
Matteo Carone ◽  
Anders Larsson ◽  
Wesley Schaal ◽  
...  
Keyword(s):  
Data Analysis ◽  
Life Science ◽  
Science Research ◽  
End Users ◽  
Scientific Workflows ◽  
Life Science Research ◽  
Cloud Environments ◽  
Container Orchestration

Containers are gaining popularity in life science research as they encompass all dependencies of provisioned tools and simplifies software installations for end users, as well as offering a form of isolation between processes. Scientific workflows are ideal to chain containers into data analysis pipelines to sustain reproducible science. In this manuscript we review the different approaches to use containers inside the workflow tools Nextflow, Galaxy, Pachyderm, 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.

scholarly journals Approaches for Containerized Scientific Workflows in Cloud Environments with Applications in Life Science

2020 ◽  
Author(s):  
Ola Spjuth ◽  
Marco Capuccini ◽  
Matteo Carone ◽  
Anders Larsson ◽  
Wesley Schaal ◽  
...  
Keyword(s):  
Data Analysis ◽  
Life Science ◽  
Science Research ◽  
End Users ◽  
Scientific Workflows ◽  
Life Science Research ◽  
Cloud Environments ◽  
Container Orchestration

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 manuscript 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.

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