Galaxy

Introduction

UF researchers now have access to an instance of Galaxy at the HPC Center - 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 HPC staff.

• To use the UF Research Computing Galaxy instance go to the UF RC instance of Galaxy.

Getting Help

• Use the UF HPC 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 om@hpc.ufl.edu
• 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 HPC biological computing support including Galaxy support are 9am to 12pm on Tue and Thr in CGRC 119.

Learn Galaxy

• 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 UF HPC BioComputing Mailing List.
• History and setup of the UF Galaxy as presented at the Galaxy Admins tele-conference.

UF HPC Galaxy specific documentation

User Access

• All users with UF HPC accounts can access and use the UF HPC Galaxy instance. The only additional setup that is required is for the Galaxy admins to add a new user to the large dataset import access list. Please contact Galaxy Admins to have it enabled.

Large Dataset Import

• Galaxy Data Import

Writing Custom Wrappers

• Galaxy Custom Wrappers

Tool Resource Request Reference

• Galaxy PBS Resource Limits

ChangeLog

• Log of changes, upgrades and fixes made in the UF Galaxy