GBrowse

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

Introduction

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. It requires a web interface to display. GBrowse has been installed on cedar and the way we installed that might be different from others. Here we explain briefly how we setup Gbrowse specifically on cedar. For more information about Gbrowse in general and how it works please take a look at Gbrowse official website: http://gmod.org/wiki/GBrowse

Gbrowse Installation

We have installed GBrowse on a server which has access to /home and /project directories of cedar. The server is called "cedar portal" and its web address is "https://gateway.cedar.computecanada.ca". On this server we have installed apache-2.4.6 web server with apache itk module. In order to be able to access files and directories of the the users while maintaining the security each research group who is interested to have GBrowse will get a specific shared account. The itk module is used to assign uid of a the shared account for each specific vhost. The GBrowse then will be installed on that vhost. Therefore for each research group we have one GBrowse instance. The GBrowse instance act as a user with uid of that shared account. In this way GBrowse is able to read files of users withing a research group.