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Tibanna: software for scalable execution of portable pipelines on the cloud

Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kirli, Burak H. Alver, Peter J. Park
doi: https://doi.org/10.1101/440974
Soohyun Lee
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Jeremy Johnson
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Carl Vitzthum
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Koray Kirli
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Burak H. Alver
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Peter J. Park
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Summary

We introduce Tibanna, an open-source software tool for automated execution of genomic pipelines on Amazon Web Services (AWS). Tibanna accepts portable pipeline standards including Common Workflow Language (CWL) and Docker, and it can be used through a simple command line interface (CLI) or Python Application Programming Interface (API). It adopts a strategy of isolation and optimization of individual executions, without pre-configured clusters. Pipelines are automatically downloaded, executed and monitored on a single local command. The versatility of Tibanna makes it ideal both for Data Commons, where data to be processed come in sparsely or in bursts, and for stand-alone large-scale parallel batch processing. Tibanna has been used to reproducibly process terabytes of genomic data for the 4D Nucleome (4DN) Network.

Availability: Source code is available on GitHub at https://github.com/4dn-dcic/tibanna.

Contact: peter_park{at}hms.harvard.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 11, 2018.
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Tibanna: software for scalable execution of portable pipelines on the cloud
Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kirli, Burak H. Alver, Peter J. Park
bioRxiv 440974; doi: https://doi.org/10.1101/440974
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Tibanna: software for scalable execution of portable pipelines on the cloud
Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kirli, Burak H. Alver, Peter J. Park
bioRxiv 440974; doi: https://doi.org/10.1101/440974

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