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Galaxy Deployment Catalog

Galaxy Deployment Catalog

Welcome to the Galaxy Deployment Catalog. This catalog describes the details of how Galaxy is installed at different institutions. Details include infrastructure information as well as user community and domain information for each deployment.

You are strongly encouraged to add your local Galaxy deployment to this catalog so that the Galaxy Community can benefit from your experience.

There are also several other sources of information about deployments. These either aren't specifically about deployment details, or they aren't organized as usefully:

Deployments: User and Domain Information

Deployment Domain Owners User Base Audience
CSIRO Galaxy Service NGS analysis: RNAseq, Genomics, metagenomics, custom tools. CSIRO 209 registered users and 30 active users
GalaxyEast Integrative 'omics data analysis IGBMC, CNRS, Inserm, Université Strasbourg
Galaxy server at the FMI NGS analysis, MA analysis, custom tools. Friedrich Miescher Institute for Biomedical Research ~130 registered users and ~40 active users wet lab scientists  
GalaxyAtUIowa Local instance at the U of Iowa IIHG Human geneticists, biologists
Idaho State University MRCF Bioinformatics, biology, next generation sequencing. Custom tools. Idaho State University Molecular Research Core Facility (MRCF) Idaho State University and Molecular Research Core Facility (MRCF) customers.
PHAC NML Galaxy NGS analysis: Molecular Epidemiology, metagenomics, viral and bacterial genomics, custom tools. PHAC NML Bioinformatics Corefacility 135 registered users and 54 active users (within last 30 days) Public Health Agency of Canada Scientists, international and local Collaborators and stakeholders
Sigenae Bioinfo-Genotoul Genomics, esp. read alignment, SNP calling and annotation, RNA-Seq, and sRNAseq Sigenae Team, GenoToul Bioinfo bioinfo gentoul and INRA researchers and collaborators  
SymD For detecting internally symmetric protein structures US National Cancer Institute (NCI) Unknown Publicly accessible 
UIUC-Galaxy General Galaxy deployment HPCBio and CNRG Hundreds, give or take UI campuses
URGI Genomics INRA ~ 30 researchers at the institution, lab members
UAB Galaxy NGS analysis: Genomics (reference and de novo), RNAseq, metagenomics, custom tools. Collaboration between Center for Clinical and Translational Science and Research Computing currently ~200 Informatics core, sequencing core, researchers and students at the institution
ZBIT Bioinformatics Toolbox Bioinformatics: SBML tools, expression data analysis, transcription factor analysis Center for Bioinformatics Tuebingen (ZBIT). Experimental biologists
deepTools Tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. Bioinformatics and Deep-Sequencing Units at the Max Planck Institute for Immunobiology and Epigenetics. Unknown Publicly accessible.
kmer-SVM Genomics, Sequence Analysis Michael Beer, Biomedical Engineering, Johns Hopkins University General Genomics Researchers 

Deployments: Implementation

Deployment Owners Server Topology Compute Memory Storage Disk Space User Management
CSIRO Galaxy Service CSIRO 2 physical, 2 virtual 32 cores on compute server 192GB on compute server SAN served from compute server to other nodes via NFS organisation’s Activity Directory
GalaxyEast IGBMC, CNRS, Inserm, Université Strasbourg Cluster 26 nodes, 400 cores 600GB Open to academic users
Galaxy server at the FMI Friedrich Miescher Institute for Biomedical Research Standalone 16 cores 132GB local attached 34TB external authentication via LDAP
GalaxyAtUIowa IIHG SGE cluster NFS University or IIHG affiliation required
Idaho State University MRCF Idaho State University Molecular Research Core Facility (MRCF) Cluster 200 cores NFS and local Customers of MRCF
PHAC NML Galaxy PHAC NML Bioinformatics Corefacility 2 virtual (1 web, 1 worker), cluster 2320 CPU cores 4640 GB NFS Users who can access the system can create their own accounts
Sigenae Bioinfo-Genotoul Sigenae Team, GenoToul Bioinfo Cluster Logins restricted and required
SymD US National Cancer Institute (NCI) Virtualized a VMware vSphere virtualized Ubuntu 12 server
UIUC-Galaxy HPCBio and CNRG Mixed-mode cluster Lots, and evolving like mad Nodes of 16GB, 24GB, 96GB, 312GB, 1TB, 2TB (SGI UV) GPFS LDAP, local users only
URGI INRA Cluster HPC cluster, 78 nodes, 854 cores 3.9 TB Using Galaxy accounts. Quotas enabled
UAB Galaxy Collaboration between Center for Clinical and Translational Science and Research Computing SGE Cluster (shared) 800+ cores
  • 2.8TB of RAM: nodes range form 16G to 385G
Lustre on QDR/DDR Infiniband, plus OpenStack. Shibboleth based institutional authn.
ZBIT Bioinformatics Toolbox Center for Bioinformatics Tuebingen (ZBIT). SGE Cluster NFS Public access
deepTools Bioinformatics and Deep-Sequencing Units at the Max Planck Institute for Immunobiology and Epigenetics. Standalone server 16 processors 141GB Directly attached Account creation is open
kmer-SVM Michael Beer, Biomedical Engineering, Johns Hopkins University Standalone

Add Your Galaxy Deployment

There are two ways to add your deployment to this catalog.

  1. Using the Wiki

    • Instance is added to the catalog immediately, but requires a wiki account
  2. Using the Google Form

    • Some delay in adding instance, and less control over what it looks like, but interface is much easier.

Using the Wiki

Have a Galaxy deployment?  The larger Galaxy community would love to learn about it.  To add a description of your Galaxy deployment to this page, you need to create a wiki page describing your Galaxy instance.  Here are the directions:

  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 your deployment.  This will become part of the URL for the page describing your deployment.  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 a description of your installation.
  5. Save, review, and edit the page until you are happy with it.
  6. Return to this page, and admire how your deployment is now included in the listings.

Using the Google Form

If the wiki option seems a little daunting, you can also describe this instance in a Google Form. Once the form has been submitted, the information will be reviewed and a catalog entry will be programmatically generated within a week or two. You will be notified via email when the entry is created.

   Describe your instance using the Google Form