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General Information

Galaxy (https://galaxyproject.org/) is a web-based platform for running scientific tools. The University of Iowa has a custom instance of Galaxy open to anyone with a uiowa email address. This instance dispatches jobs to the High Performance Computing (HPC) Neon cluster (https://wiki.uiowa.edu/display/hpcdocs/Neon+Overview+and+Quick+Start+Guide).

If you are new to Galaxy, you may want to consider attending one of the short summer courses hosted by the Iowa Institute of Human Genetics (IIHG Galaxy/Bioinformatics Education). These courses include hands-on Galaxy training.


Accessing Galaxy

To use the University of Iowa's instance of Galaxy, go to https://research-galaxy.hpc.uiowa.edu:44321/ and log in with your uiowa email address and Hawk ID password. Galaxy will automatically create an account for you if you don't already have one. You can then upload your data and start running tools/ workflows.

If you are not on a UI network, you may need to connect to Galaxy via VPN. See http://its.uiowa.edu/support/article/1876 for VPN setup instructions.

To upload files to Galaxy using the FTP protocol, please connect to research-galaxy.hpc.uiowa.edu on port 22021 using the 'sftp' command line tool, WinSCP (Windows), Cyberduck (Mac) or similar. Log in using your Hawk ID and Hawk ID password. After successfully logging in, change to the directory named the same as your Hawk ID.


Learning Resources

Galaxy tutorials and screencasts from the Galaxy Project Wiki: https://wiki.galaxyproject.org/Learn

2015 IIHG Bioinformatics Short Course- Galaxy hands-on training: https://wiki.uiowa.edu/download/attachments/143640370/GalaxyTraining-20150519.pdf

2014 IIHG Bioinformatics Short Course- Galaxy hands-on training: https://wiki.uiowa.edu/display/galaxyusers/Galaxy+2014

2013 IIHG Bioinformatics Short Course- Using Galaxy to manipulate large datasets: http://medicine.uicapture.uiowa.edu/Panopto/Pages/Viewer/Default.aspx?id=ae554e6c-38e8-4d28-b6ee-3a22de4c5165

2013 IIHG Bioinfomatics Short Course II- Galaxy intro and file formats: https://wiki.uiowa.edu/download/attachments/89463895/bioinformatics_short_course_II.pdf

2013 IIHG Bioinfomatics Short Course II- Galaxy basics: https://wiki.uiowa.edu/download/attachments/89463895/Galaxy_Overview_Bioinformatics_Course.pdf

2012 IIHG Bioinformatics Short Course- Using Galaxy to manipulate large datasets: https://wiki.uiowa.edu/download/attachments/80413422/Lab1_Instructions.pdf

 

Basic Troubleshooting

  • Galaxy webpage isn't loading:
    • Verify that you are on a UI network or connected via VPN (see Getting Started section for VPN instructions.) Make sure you are using the correct URL.
  • Can't log in:
    • Anyone with a valid HawkID and password should be able to log in- no manual setup required. Verify that your HawkID works by going to http://hawkid.uiowa.edu/ and clicking "Test Your Account".
  • Job isn't running/ is taking a while to start running:
    • Jobs are dispatched to the HPC Neon cluster and scheduled via Sun Grid Engine. Jobs can take a while to start running, depending on Neon availability. If you have a Neon account, you can check whether your job is queued yet, and its priority, by logging onto Neon and running "qstat -u rchgx".
  • Job failed:
    • To view the error that caused the job to fail, click on the "View or report this error" icon in the history entry for the job. If the error is produced by the tool, see https://wiki.galaxyproject.org/Support#Error_from_tools for troubleshooting steps. If this doesn't solve the issue, or if the error is a cluster error or otherwise not produced by the tool, please report the error by clicking on the "View or report this error" icon and submitting an error report.

 

Support

For UI Galaxy support requests, please contact iihg-galaxy-admin@uiowa.edu.

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