Galaxy

UF researchers now have access to an instance of Galaxy at the Research Computing - a web-based framework for accessible, reproducible and transparent biological computing. Galaxy has arisen as the most popular framework for providing biological researchers access to the tools they need for the analysis of their data. It helps researchers survive and thrive in the face of ever growing computational and data management demands of the contemporary biology. It also provides the convenience of a robust system of user account handling, data sharing and security. Since most biological research projects now happen in a distributed collaborative environment Galaxy's work history sharing and analytical pipeline building as well as publishing and sharing the results in a convenient and secure manner address the most important issues and allow UF researches to be highly competitive. Other benefits an UF instance of Galaxy are access to high-speed campus Research Network, using large HPC cluster resources for running jobs, transparent user account access and convenient data upload as well as full system and user support by the RC staff.

UF Galaxy URI

Access the UF RC instance of Galaxy.

Getting Help

• Use the UFRC Support Ticket System to request adding new tools or reference data to the Galaxy and to file problem reports. Note: If you are submitting a problem report the first step should be to share the history that contains a failed step with by using the 'bug' icon in galaxy.
• When submitting a problem report use the Galaxy bug reporting tool to provide us with the information necessary for solving the problem. Click on the green "bug" icon in the problematic step in the history and submit the resulting form. This tool automatically shares your history with us, so you don't have to share it separately. Alternatively, you can just share your Galaxy history if necessary.
• UFGI Office hours for UFRC biological computing support including Galaxy support are 9am to 2pm on Tue and Thr in CGRC 119.

Learn Galaxy

• UFRC Training sessions on using Galaxy take place every semester. See the schedule.
• The main documentation site for galaxy users is the Galaxy Wiki/Learn.
• The main mailing list for users of Galaxy is "Galaxy Users"].
• There is also a UFRC BioComputing Mailing List.
• History and setup of the UF Galaxy as presented at the Galaxy Admins tele-conference.

UFRC Galaxy specific documentation

User Access

• All users with UFRC accounts can access and use the UFRC Galaxy instance.

Large Dataset Import

• Create your Galaxy upload directory as '/ufrc/apps/galaxy/incoming/<your email address in galaxy>' and copy your datasets there. Note, it may take up to 15 minutes for Galaxy to fix the permissions before uploaded files will become available in a list at the bottom of the Galaxy 'Get Data > Upload File' tool.
• Use the 'Upload File' tool and either upload smaller files from your local machine or select files in your galaxy incoming directory by clicking on the checkboxes in front of the file names and click on the 'Execute' button to start the upload.

Writing Custom Wrappers

• Galaxy Custom Wrappers

Known Galaxy Problems

• Galaxy Known Issues

Report a Galaxy Problem

• How to Report a Problem

Share a History

• Share your Galaxy history

Administration

• Notes on Galaxy_Configuration for instance administrators.