Snakemake Cloud Pipelines

Location: 
CG Auditorium
Speaker: 
Vanessa Sochat

Reproducible science is contingent on the ability to execute a workflow once, and easily share software and workflow dependencies to run again. This presents a significant problem in the case of disparate environments, as there is large variance in executors afforded by such environments. Snakemake, enables the scientific user to represent an entire workflow in a transparent and readable way, while providing seamless execution on single computers, cluster environments and the cloud [1]. For this talk, I will demonstrate how to create a scientific workflow using Snakemake, and how to execute it in a local cluster and cloud environment.

[1] Köster, Johannes, and Sven Rahmann. 2012. “Snakemake--a Scalable Bioinformatics Workflow Engine.” Bioinformatics 28 (19): 2520–22. [link]

Speaker Description: 

Vanessa Sochat is a research software engineer in the Stanford Research Computing Center.

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