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Galaxy: Overview

Galaxy @ USC

Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research.  It integrates hundreds of popular statistical and bioinformatical tools for genomic sequencing data analysis. 

Accessing Galaxy public server is hindered by the data file size limit, slow speed, as well as data security.  To help USC users to truly take advantage of this powerful platform, we have implemented a local instance for campus-wide access, as well as a docker build version that allows users to install and use the Galaxy on their own desktop and even laptop computers.

Main Features

Galaxy provides a platform for hundreds of cutting-edge tools that can be used to perform many types of analysis, particularly for next-generation sequencing (NGS) data.  Both our local Galaxy server and Galaxy docker build contain many very useful and well-cited open access tools, which nicely complement our licensed commercial software. 

  • RNA-seq: DESeq2, edgeR, StringTie, HISTAT2, Sailfish 
  • ChIP-seq: macs2, Cistrome, SICER, 
  • SAMtools, Picard,
  • DeepTools, NGSPlot
  • more...

Access Galaxy @ USC

There are three ways to use our customized Galaxy:

1. On your own lab/office computers

  • Install our Docker Build Galaxy on your own lab/office computers for secure, convenient, and exclusive access
  • The performance of the Galaxy is limited by the hardware of your computers
  • Mandatory registration is required for installing Docker Build Galaxy on your own computers.  Please complete Local Installation Form.

2. On workstation computers in the libraries

The Docker Build Galaxy has been installed on multiple workstation computers at:

  • Norris Medical Library (RM203A), the Health Sciences Campus.
  • Wilson Dental Library,  the University Park Campus.
  • First-time user must submit the Galaxy Workstation Request Form

3. USC Galaxy Server (Coming November 2017)

  • Implemented on a Dell PowerEdge R630 server (Dual 12-core Intel Xeon processors, 512GB RAM), coupled with a 50 TB NAS storage space (RAID6) for robust performance when handling large data sets.
  • Web browser access with dedicated user account and disk quota.
  • Accessible from any computers on USC network.  Off campus access requires a USC VPN connection.
  • First-time user must submit the USC Galaxy Server Access Request Form

Need Help?

Galaxy Tutorials and User Support

Help @ USC Libraries Bioinformatics Service

  • Report errors by submitting Galaxy Bug Report
  • Request Galaxy tools to be enabled in our Galaxy by submitting Galaxy Tools Request Form
  • Email us: nmlbio@usc.edu