Galaxy

Introduction

Galaxy is an open source, web-based platform for data intensive biomedical research. It is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.

Galaxy on Cedar

On cedar we provide one galaxy instance for every research group. Galaxy installation requires a special setup that needs to be done by Compute Canada (CC) staff. If you need Galaxy for your group please write an email to support team.

Galaxy Directory Structure

Galaxy is usually installed on the project directory of the group and it contains several sub-directories. The name of the Galaxy top directory is determined by taking the first two character of PI username + "glyx". For example if PI username is "davidc" the galaxy top directory will "daglxy" and it is located in /project/group name/ were group name is the group name of PI, eg., def-davidc. Galaxy main directory contains the following sub-directories which is slightly different than the original galaxy package.

• config: It contains all require configure files to setup and optimize Galaxy. Bellow we will explain some basis concept of some of configure files that need sto be setup in our HPC environment, however, we are not able to cover all concepts as they are out of this scope. In original galaxy package this directory is located within galaxy directory.
• galaxy: It contains the core python scripts of Galaxy.
• logs: Contains all log files during server Stop/Start/Run process as well as. The most important file in this directory is galaxy.log that is widely used to diagnose issues during Galaxy run.
• plugins: Contains all plugins. In original galaxy package this directory is located within galaxy directory.
• tmp: Contains all temporary files that galaxy needs for compiling and installing tool sheds.
• venv: It is a python virtual environment directory and it contains all python package dependencies.
• tool-data: It contains data used by tools See the samples in data-integration
• tool-dependencies: It contains all dependency packages that is needed for tool sheds. By default packages in this directory are being installed using anaconda.
• database: It contains input/output and error files of all job that run in cluster nodes.

Galaxy Files ownership and modification

All files of your galaxy instance belongs to a "pseudo account" or "shared account" that is generated by admin at installation time. pseudo accounts do not belong to a real users but they belong to a specific group. They never expired and everyone within the group is able to login as pseudo account using SSH key. The name of the pseudo account in this case is the same name as the top galaxy directory explained above. In order to modify any file you first need to login as "pseudo account"

Galaxy Server

Galaxy server cannot be run on cedar, please do not run startup script on cedar. Instead we use another machine (called gateway) that contains a web server with all cedar /project and /home mounted. SSH connection to this machine by users is not possible due to the security reason but you can start, stop or run your Galaxy server by going to website [1] and follow Galaxy link.