IGB Developer's Guide
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Table of Contents

Introduction

The following instructions assume you are not going to make a new genome version directory and that all you need to do is update a refGene data set.

For many genomes supported by UCSC, the refGene data collection from UCSC represent the canonical gene model annotations for that genome. 

IGB QuickLoad main IGB QuickLoad site is configured so the canonical gene models annotations are loaded into IGB as soon as the user selects the corresponding genome version.This  This is configured through the annots.xml file that resides in every genome version directory. Any data set with attribute "load_model" set to "Whole Genome" will automatically load into IGB.

For

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many genome versions, the canonical gene models are provided by UCSC Genome Bioinformatics from their refGene data collection. This refGene collection gets updated from time to time, and so it is important for users that we update the main IGB Quickload site when UCSC updates their data. This ensures that what users see in IGB matches what they see in the UCSC Genome Browser software.  
The following instructions explain how to update this file. The instructions assume you are not going to make a new genome version directory and that all you need to do is update a refGene data set.


Note

As of IGB 10.1.0 most UCSC genome versions and tracks should now be available by default in IGB via the UCSC REST data provider.


Understand IGB QuickLoad naming conventions

Note

IGB QuickLoad file names should include the genome version and the UCSC table name. The title in the annots.xml file should match the track name but should not include the species name, as that will be obvious to the user and may make linkout patterns harder to maintain.

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However, the UCSC genome browser sometimes include species names in the title of its mRNA track. IGB QuickLoad data sets should not include species names in the titles. For example, the title of an mRNA track is always "mRNA" and never (for example) "Zebrafish mRNA."

Command-line utilities you'll need

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  • tabix and bgzip from htslib 
  • git
  • svn
  • UNIX wget (not installed by default on Mac but available on most other UNIX systems)
  • UNIX sort
  • UNIX gunzip

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Code Block
$ git pull origin mastermain-JDK8

Use svn to get a copy of the QuickLoad data repository: TO BE UPDATED

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