Troubles launch IGV on Linux(Debian)
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Entering edit mode
9 weeks ago
PoscaXVIII • 0

I am trying to run IGV on Debian.

I have followed this steps

  1. wget https://data.broadinstitute.org/igv/projects/downloads/2.16/IGV_Linux_2.16.2_WithJava.zip
  2. unzip IGV_Linux_2.16.2_WithJava.zip
  3. My@machine:~/software/IGV_Linux_2.16.2$ ./igv.sh

And this is the output I got

WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
openjdk version "11.0.13" 2021-10-19
OpenJDK Runtime Environment Temurin-11.0.13+8 (build 11.0.13+8)
OpenJDK 64-Bit Server VM Temurin-11.0.13+8 (build 11.0.13+8, mixed mode)
INFO [Sep 26,2023 11:07] [Globals] Development mode is enabled
INFO [Sep 26,2023 11:07] [Main] Startup  IGV Version 2.16.2 07/14/2023 12:24 AM
INFO [Sep 26,2023 11:07] [Main] Java 11.0.13 (build 11.0.13+8) 2021-10-19
INFO [Sep 26,2023 11:07] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Sep 26,2023 11:07] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-11.0.13+8   
INFO [Sep 26,2023 11:07] [Main] OS: Linux 6.1.0-12-amd64 amd64
INFO [Sep 26,2023 11:07] [Main] IGV Directory: /home/antoine/igv
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Sep 26,2023 11:07] [CommandListener] Listening on port 60151
INFO [Sep 26,2023 11:07] [GenomeManager] Loading genome: https://s3.amazonaws.com/igv.org.genomes/hg19/hg19.json
INFO [Sep 26,2023 11:07] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz    

IGV program can be launch but the windows is unusable (frozen black screen) see below screenshot

IGVscreen

Any idea how to fix this issue?

IGV • 658 views
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0
Entering edit mode

Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem.

I have had this kind of shadowing when I ssh-ed into an instance and X11 tunneled the graphics. My IGV was working but my tracks were shadowed like you posted.

1) I realised the shadowing happened when there is a window from the local machine open in the back and X11 pops out over that. I always moved my IGV into an empty second monitor.

2) I tried an older IGV version and often stick with that one. Didnt get the updates but at least have working IGV.

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Entering edit mode

Hi, Thank you for your help. I tried both of your suggestions. Regardless of the version installed (tried 4 different versions), the result always remains the same. The software seems to work but the graphical display is completely unusable, as you mentioned.

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0
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Your log seems fine.

Could you add the results of these commands?

  • Which version of debian are you on?

      lsb_release -c
    
  • Are you on wayland or xorg?

      echo $XDG_SESSION_TYPE
    
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0
Entering edit mode

Here the output I got

    MyPC@Debian:~$ lsb_release -c
No LSB modules are available.
Codename:   bookworm
MyPC@Debian:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description:    Debian GNU/Linux 12 (bookworm)
Release:    12
Codename:   bookworm

I know that people with the same output (after run ./igv.sh) were able to use IGV normally.

I am on wayland. Is this a problem?

Thanks for your help

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Entering edit mode
8 weeks ago
barslmn ★ 2.0k

I am on wayland. Is this a problem?

Could be.

Can you try it with Xorg? You can usually change to Xorg in your login manager.

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Entering edit mode

Hi barslmn, Thank you so much for your help it works perfectly. No more frozen black screen. I just changed from wayland to Xorg (On the password screen of Linux sessions, you will find a cogwheel icon at the bottom-right corner).

Any idea why IGV doesn't like it?

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0
Entering edit mode

Great it worked out.

Any idea why IGV doesn't like it?

No idea but i don't think its on IGV. Wayland is a newer display server for linux and has some compability issues in general. Xorg is the mature solution.

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