Warning
Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.
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.
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
The IGV user guide is available online at https://www.broadinstitute.org/igv/UserGuide
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
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