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VirtualAppliances

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Virtual Appliances

One of the many ways that Galaxy is available is in virtual appliances that already have Galaxy installed and configured on them - these may take the form of cloud images, more traditional virtual machine images, or docker containers. Running a pre-configured Galaxy virtual appliance saves on installation and configuration work, and enables you to get up and running with Galaxy very quickly.

These virtual appliances are frequently used for training, or as tool demonstration and data publishing platforms. However, they not limited to teaching, tool demonstration, and data publishing. Production scale/quality Galaxy servers are also deployed using them.

Galaxy Virtual Appliance Platforms

Cloud Images

Cloud images are virtual appliances that run on cloud infrastructures.

Amazon Web Services

Amazon Web Services-based Galaxy CloudMan instances use an Amazon Machine Image (AMI) (a type of VM specific to AWS) when creating Galaxy servers. Some appliances are available via AMIs. Using Galaxy via AMIs will leverage Amazon's hardware resources and can potentially scale quite well.

Virtual Machine Images

Virtual Machine Images

Some virtual appliances are packaged for VirtualBox - a free virtualization platform available for many operating systems including Windows and Mac OS X. Some may also be used within the VMware ecosystem - which has a variety of free and commercial virtualizaiton products.



Docker

Docker Containers

Docker is a potentially more light-weight alternative to virtualization. Docker-based appliances are available as runnable containers registered in Docker Hub, but also as open source Dockerfiles which serve as a reference for exactly how to build the container and allow one to rebuild the container from scratch and potentially with customizations. Docker is available on newer Linux distributions and on Windows and Mac OS X using Boot2Docker

Galaxy Virtual Appliance Directory

This lists all known available Galaxy virtual appliances. The goal is to make it easy for the Galaxy community to find and deploy them, thus benefiting from the (generous!) work of others.

Appliance Technology Domains Description Owners Date Created/Updated
DDBJ Read Annotation Pipeline VM Reference genome mapping, de novo assembly, and structural and functional annotations VirtualBox VM created in 2015 so that "Researchers may utilize the virtual machine image for users’ sensitive datasets such as human personal genomic sequences." DDBJ Read Annotation Pipeline, Development team 2015
RNAmapper VM, AMI Identify genome region linked to a mutation, and causal candidate mutations RNAmapper uses RNA-seq data to identify both a region of the genome linked to a mutation as well as candidate mutations that may be causal for the phenotype of interest. Moens Lab, Fred Hutchinson Cancer Research Center; Megason Lab, Harvard Medical School 2012/08/03
MegaMapper VM, AMI positional cloning of mutations MegaMapper is a computational pipeline for positional cloning of mutations by whole genome sequencing. Megason Lab, Harvard Medical School 2013/05/02
Automated Selection of Hotspots (ASH) VM hotspot detection automated detection quantitative ranking of hotspots to support histopathologists in selecting the ‘hottest’ hotspot areas in adrenocortical carcinoma. David van Zessen <d.vanzessen@erasmusmc.nl>, Erasmus Medical Center 2014/05/16
UC Davis Bioinformatics Core Training Galaxy AMI Training Includes all needed tools and datasets for a weeklong workshop. UC Davis Bioinformatics Core 2014/06/20
Immunoglobulin Galaxy VM immunoglobulin a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts. David van Zessen <d.vanzessen@erasmusmc.nl>, Erasmus Medical Center 2014/08/19
ballaxy Docker computer aided drug design, molecular modelling Contains the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. Hans-Peter Lenhof Lab, Saarland University; Oliver Kohlbacher Lab, University of Tübingen; Andreas Hildebrandt Lab, University of Mainz 2014/09/02
Pitagora-Galaxy VM, AMI General Purpose Includes the tools and workflows that are described at our wiki. Genome Science Division, RCAST, University of Tokyo 2014/11/20
SADI-Galaxy Container Docker Web services, RDF Make SADI services available in a Galaxy platform. Mikel Egaña Aranguren 2015/01/07
RNA Galaxy Workbench Docker RNA-Seq A Docker based RNA-Seq workbench RNA Bioinformatics Center, part of the German Network for Bioinformatics Infrastructure (de.NBI). 2015/02/17
RNAcommender Docker RNA-protein interactions Genome-wide recommendation of RNA-protein interactions. Gianluca Corrado, Andrea Passerini 2016/08/08

Add a Virtual Appliance

Have you created or know of a virtual appliance that could be useful to the Galaxy community? Then please share it! This will help others and also help get the word out about the resource.

There are two ways to add a virtual appliance to this directory.

Submit an Online Form

If the wiki option seems a little daunting, you can also describe this resource in this form. Once the form has been submitted, the information will be reviewed and a virtual appliance page will be created within a week. You will be notified via email when the page is created.

   Submit a virtual appliance using the form   

Use the Wiki

To add a virtual appliance to this directory, create a wiki page describing the appliance:

  1. Login to the wiki. If you don't have an account, you'll need to create one.

  2. Pick a good descriptive, CamelCase name for the appliance.  This will become part of the URL for the page describing the appliance.  Avoid embedded spaces as they make lousy URLs.

  3. Type the CamelCase name in box below and hit the "Create" button.

  4. A template for the new page will appear.  Replace the template text with details about the appliance.
  5. Save, review, and edit the page until you are happy with it.
  6. Return to this page, and review how the resource appears in this listing.