Open AccessTibanna: software for scalable execution of portable pipelines on the cloud
Author(s) -
Soohyun Lee,
Jeremy Johnson,
Carl Vitzthum,
Koray Kırlı,
B. Alver,
Peter J. Park
Publication year - 2019
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btz379
Subject(s) - computer science , python (programming language) , workflow , cloud computing , scalability , source code , software , operating system , pipeline transport , software engineering , terabyte , pipeline (software) , open source , database , scheduling (production processes) , programming language , operations management , environmental engineering , engineering , economics
We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network.
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