Troubles running IGV on a server.

Question

[ManuelDB]

I am trying to run IGV on a server.

I have followed this steps

• XQuartz installed
• ssh into me server with the -Y flag, e.g. ssh [e-mail] -Y ( I have also tried -X)
• I have started IGV on the remote server with the supplied igv.sh

And this is the output I got. In the end, nothing happens. What am I doing wring?

 WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
openjdk version "11" 2018-09-25
OpenJDK Runtime Environment 18.9 (build 11+28)
OpenJDK 64-Bit Server VM 18.9 (build 11+28, mixed mode)
WARN [2022-03-29T19:47:47,408]  [Globals.java:139] [main]  Development mode is enabled
INFO [2022-03-29T19:47:47,468]  [DirectoryManager.java:179] [main]  IGV Directory: /home/mdb1c20/igv
INFO [2022-03-29T19:47:49,965]  [Main.java:156] [AWT-EventQueue-0]  Startup  IGV Version 2.7.0 10/08/2019 12:45 AM
INFO [2022-03-29T19:47:50,016]  [Main.java:157] [AWT-EventQueue-0]  Java 11 (build 11+28) 2018-09-25
INFO [2022-03-29T19:47:50,017]  [Main.java:160] [AWT-EventQueue-0]  Java Vendor: Oracle Corporation http://java.oracle.com/
INFO [2022-03-29T19:47:50,017]  [Main.java:162] [AWT-EventQueue-0]  JVM: OpenJDK 64-Bit Server VM 18.9   
INFO [2022-03-29T19:47:50,017]  [DirectoryManager.java:84] [AWT-EventQueue-0]  Fetching user directory... 
INFO [2022-03-29T19:47:50,253]  [Main.java:165] [AWT-EventQueue-0]  Default User Directory: /home/mdb1c20
INFO [2022-03-29T19:47:50,254]  [Main.java:166] [AWT-EventQueue-0]  OS: Linux 3.10.0-1160.36.2.el7.x86_64 amd64
INFO [2022-03-29T19:47:50,708]  [Main.java:212] [Thread-2]  A later version of IGV is available (2.12.2)
INFO [2022-03-29T19:47:54,465]  [GenomeManager.java:195] [pool-3-thread-1]  Loading genome: /home/mdb1c20/igv/genomes/hg19.genome
INFO [2022-03-29T19:47:58,134]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2022-03-29T19:47:58,152]  [GenomeManager.java:287] [pool-3-thread-1]  Genome loaded.  id= hg19
INFO [2022-03-29T19:47:58,164]  [CommandListener.java:120] [Thread-4]  Listening on port 60151

[GenoMax]

Have you verified that the $DISPLAY variable is correctly set on server end? Are you able to run a simple xterm command and have that window pop back up on your local mac?

With Xquartz I have discovered that it is safer to log in to the server using the terminal included in XQuartz. External terminal programs don't seem to reliably work with XQuartz in some OS version dependent fashion.

[ManuelDB]

If I run xterm in the server I get this message

 xterm: Xt error: Can't open display: 
xterm: DISPLAY is not set

[GenoMax]

That means your $DISPLAY variable on server-side is not getting set correctly. This is the virtual terminal where all graphics output from the server will be redirected.

You can try logging in via XQuartz terminal and see if that fixes the issue.

[ManuelDB]

Thanks for your help.

I have followed your indication and yes I can open IGV. However, when I move the mouse, the window becomes black

In the screenshot I have shown below there is some color but on my screen is black and nothing really I can do with the application open.

[GenoMax]

X11 connections require good network connectivity. If you have limited bandwidth then X11 is not going to work well. I assume you are doing this remotely (i.e. you are not on the same network as the server).

[ManuelDB]

Yeah, I am doing this remotely.

Many thanks, GenoMax for all your support!

[GenoMax]

You may be best off downloading the BAM file locally to view if you are unable to make IGV work via X11. There are text based browser options that you could try on the server : https://github.com/dariober/ASCIIGenome