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The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are joining together for a unified event to be held in Portland, Oregon, United States, June 25-30, 2018.  The event features two days of training, a two day meeting, and finish with two or four days of intense collaboration at the GCC OBF CollaborationFest Core and Encore events.  The meeting will feature joint and parallel sessions, and shared keynotes, poster and demo sessions, and social events.  Colocating GCC and BOSC will bring together the widest possible community of bioinformatics developers and practitioners into a single place.  At this event the whole will be greater than the sum of the parts.

The event is organized by Oregon Health & Science University and will be held at Reed College, a small liberal arts college in Portland. Conference housing is available in two Reed College residence hall complexesPortland is a vibrant city in the American Northwest, close to the Cascade Mountains, the Oregon Coast, and the Columbia River. 

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Tuesday, June 26 • 3:30pm - 6:00pm
GATK4: What's new and how to run it

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Key:  BB | XB |  -  |  -  | GG | CL

The advent of open, portable workflow languages is an exciting development which allows for the definition of a workflow to be decoupled from the execution. One can create workflows which can run unmodified on local compute, HPC clusters, or the cloud. As these languages are not tied to a specific execution environment, the descriptions can easily be shared, discovered and even composed together to form more complex workflows. The Workflow Description Language (WDL) is an open, community driven standard that is designed from the ground up as a human-readable and -writable way to express portable tasks and workflows.

In this session we’ll walk through the lifecycle of writing, sharing and discovering portable workflows in WDL. We’ll introduce the WDL syntax. You’ll learn how to write and run a workflow locally. We’ll demonstrate how to use EPAM’s Pipeline Builder toolto visualize WDL workflows. We’ll look at Dockstore, an open platform where one can publish, share and discover workflows. Finally we’ll put everything together and see how we can compose workflows we find on Dockstore together with our own additions to create new, more powerful workflows.


  • Mac or Linux computer
  • Java 8 installed and runnable from the command line
  • A workshop bundle downloaded from TBD

avatar for Geraldine Van der Auwera

Geraldine Van der Auwera

Associate Director of Outreach and Communications, Broad Institute
I run outreach and communication efforts to the global scientific research community on behalf of the Data Sciences Platform (DSP) at the Broad Institute. My team's efforts include technical support, documentation, social media presence and user education events for users of soft... Read More →

Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 2