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Bioinformatics Software: Galaxy

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.

USC Galaxy Server vs. Docker-Galaxy

USC Galaxy server is a full-fledged Galaxy platform. 

  • Based on January 2019 official release (v 19.01)
  • Faster data upload/download within USC network
  • Shorter analysis queues
  • Tools offered through Partek Flow are purposely removed 

Docker-Galaxy is a lighter version of Galaxy that can be installed on your own computer.  

  • Based on January 2018 official release (v 18.01)
  • Analyze sensitive data on your own computer
  • Heavily customized toolbox focusing on ChIP data analysis
  • Requires a powerful computer (fast CPU, large RAM and a minimum of 200GB storage for installation) for installation and data analysis. 

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, HISAT2, Sailfish, featureCount
  • ChIP-seq: MACS2, diffBind, CEAS, Cistrome
  • Variant analysis: SnpEff, SnpSift, VCFtools
  • NGS utility tools: BAMtools, BEDtools, Picard, SAMtools
  • QA/QC and visualization: FASTQC, deepTools, ngs.plot
  • more...

Use the comparison chart to find out which NGS analysis platform available at USC better serve your NGS analysis needs. 

Access Galaxy @ USC

There are three ways to use our customized Galaxy:

1. USC Galaxy Server (January 2019, v19.01)

  • 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.

2. On your own MAC/Linux computers

  • Install our Docker-Galaxy (January 2018, v18.01) on your lab/office computers for secure, convenient, and exclusive access
  • Performance of the Galaxy is limited by the hardware of your computers
  • Minimum requirements: 200GB free storage

3. On workstation computers in the libraries

  • Docker-Galaxy (January 2018, v18.01) has been installed on multiple workstation computers at:
  • Norris Medical Library (NML 203A), Health Sciences Campus.
  • Center for Electron Microscopy & Microanalysis (CEM 202), University Park Campus.

Registration is required to all first-time users: Galaxy Access Request form

Need Help?

Galaxy Tutorials and User Support

Help @ USC Libraries Bioinformatics Service