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Cloud-based workflow and tool execution using Toil and sharing via the Dockstore

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Published on Oct 20, 2016

Brian O’ Connor
Technical Director, Analysis Core

Dr. O’Connor led the technical development of the cloud infrastructure for the International Genome Consortium’s PanCancer Analysis of Whole Genomes distributed analysis project. For this project he was responsible for the creation of infrastructure that analyzed 5,800 genomes across 14 cloud and HPC environments. The software built for this, Consonance and the Dockstore, are now open source and used by members of the community. Dockstore (http://dockstore.org) has become a reference implementation for the GA4GH and has received wide praise as a method of sharing tools and workflows in a platform and cloud agnostic way.

Creating mobile workflows and tools is a challenge for genomics researchers. In this talk I will describe the efforts of the GA4GH Containers and Workflows task team in creating a standard for this. I will detail the creation of the Dockstore, our best-practice platform for exchanging workflows and tools using Docker. Finally, I will provide an update on the Toil project which is a platform for running tools and workflows at scale on AWS and other clouds. The latest Toil recompute of 20,000+ RNASeq samples shows the power of combining Docker-based tools with a highly scalable workflow engine.

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