Warning

Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.

Integrative Genomics Viewer (IGV)¶

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Interactive Usage¶

After connecting to Iceberg (see Establishing a SSH connection), start an graphical interactive session with the qsh command. In testing, we determined that you need to request at least 7 Gigabytes of real memory to launch IGV

qsh -l rmem=7G

The latest version of IGV (currently 2.3.63) is made available with the command

module load apps/binapps/igv

Alternatively, you can load a specific version with

module load apps/binapps/igv/2.3.63

This command makes the IGV binary directory available to your session by adding it to the PATH environment variable. Launch the applications with the command

igv.sh

Documentation¶

The IGV user guide is available online at https://www.broadinstitute.org/igv/UserGuide

Installation notes¶

A binary install was used

unzip IGV_2.3.63.zip
mkdir -p /usr/local/packages6/apps/binapps/IGV
mv ./IGV_2.3.63 /usr/local/packages6/apps/binapps/IGV/2.3.63
rm /usr/local/packages6/apps/binapps/IGV/2.3.63/igv.bat

Modulefile¶

The module file is on the system at /usr/local/modulefiles/apps/binapps/igv/2.3.63

Its contents

#%Module1.0#####################################################################
##
## IGV 2.3.63 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
        puts stderr "Makes IGV 2.3.63 available"
}

set version 2.3.63
set IGV_DIR /usr/local/packages6/apps/binapps/IGV/$version

module-whatis   "Makes IGV 2.3.63 available"

prepend-path PATH $IGV_DIR