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Wednesday, June 29 • 3:15pm - 4:30pm
D02: The Genomics Virtual Lab - A turnkey Galaxy platform for the cloud

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Authors
  • Enis Afgan - Johns Hopkins University
  • Clare Sloggett, Nuwan Goonasekera, Simon Gladman, Yousef Kowsar, Andrew Lonie - Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne
  • Igor Makunin, Derek Benson, Michael Pheasant, Ron Horst - Research Computing Centre, University of Queensland.
  • Mark Crowe - Queensland Facility for Advanced Bioinformatics (QFAB), University of Queensland

Abstract

Australia’s researchers have access to a national cloud (NeCTAR) comprising 30,000 cores. To maximize the utility of this cloud to the growing number of genomics researchers, we have developed the Genomics Virtual Laboratory (GVL). The GVL allows anyone to create and launch a scalable, flexible personal cluster which all the key components preconfigured, which can be deployed on Openstack, Amazon and soon Google. It supports three user interfaces: the browser, SSH command line, and VNC desktop. Preinstalled web applications include Galaxy, RStudio, Jupyter Hub, Pacbio SMRT Portal, and Web Apollo. Under the hood Linuxbrew provides hundreds of command line and GUI bioinformatics tools. All in all, the GVL provides a turn-key solution for most bioinformatics tasks on the cloud.

In our GVL demonstration we will:
  • Launch different flavours of the GVL instance on various clouds
  • Show the various components of these GVLs
  • Import data from GenomeSpace into Galaxy
  • Use tools installed via Galaxy on the command line
  • Access the Galaxy filesystem from the command line
  • Describe how custom flavours of the GVL can be built via Ansible scripts
  • Discuss the success of GVL as a training platform

Presenters
avatar for Simon Gladman

Simon Gladman

Bioinformatician, VLSCI / University of Melbourne

Attendees (9)