How to use IGV on Unity

Install

1. Navigate to cd /work/pi_hputnam_uri_edu/pgrams
2. Request interactive node usage using salloc
3. Navigate to the IGV download page, and right click “IGV for Linux” > “Copy Link Address…”
   1. https://igv.org/doc/desktop/#DownloadPage/
   2. https://data.broadinstitute.org/igv/projects/downloads/2.19/IGV_Linux_2.19.1_WithJava.zip
4. Download the IGV Linux application into this directory: wget https://data.broadinstitute.org/igv/projects/downloads/2.19/IGV_Linux_2.19.1_WithJava.zip
5. Unzip the application: unzip IGV_Linux_2.19.1_WithJava.zip

Running the program

1. When ssh-ing into Unity, add -X to your ssh command: ssh -X username_uri_edu
2. Navigate to cd /work/pi_hputnam_uri_edu/pgrams/IGV_Linux_2.19.1/
3. “To run an application on the cluster that uses a GUI, you must use an interactive job, in addition to the –x11 argument”: salloc -c 6 -p cpu --x11
4. Run program by ./igv.sh
   1. I had some issues with how XQuartz was rendering the window for me, so I had to run this:

export _JAVA_OPTIONS='-Dsun.java2d.uiScale=1.0 -Dsun.java2d.xrender=false -Dsun.java2d.opengl=false'
export LIBGL_ALWAYS_INDIRECT=1
./igv.sh

Notes

It’s still kinda slow. Which almost defeats the purpose, but allows for viewing bam files without having to download them.