Can't build IGB on Debian (Originally posted to IGB Jira)

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IGB Helper

Jun 15, 2020, 11:04:51 PM6/15/20
to Integrated Genome Browser Help Desk

On March 20, an IGB user reported problems compiling IGB on a Debian machine:

I was trying to compile IGB on my debian machine. I unfortunately encountered an error. Please see the two log files with full stack trace and full debug logging: one with -DskipTests=true (IGB.log) and one without (IGB_skip.log). Is there anything I could do?

After looking at the attached logs, we're realized the problem was that the JavaFX library was not available. 

After a few email exchanges, we received the following update:

Thanks for replying about my reported issue. Indeed, it was a problem related to JavaFX. Java was already installed on my machine but running those two commands solved the issue:
apt-get install openjdk-8-jdk openjfx

Chester Dias

Jul 14, 2020, 11:49:39 AM7/14/20
to Integrated Genome Browser Help Desk

Cause of Error:

igb-javafx-util: Compilation failure

This package needs java fx to be present.



Below commands to be run on the terminal for installation of Java and JavaFX on Debian 9(Stretch)


sudo apt-get update

sudo apt update

sudo apt-get install openjdk-8-jdk

sudo apt-get install openjfx


Below are steps for installation of Java and JavaFX on Debian 10

Note: Debian 10 does not seem to have openjdk in its default repositories.


1. Download the Correct Java from


2. Run the following commands on the terminal from the directory containing the above-downloaded JDK.


sudo mkdir -p /usr/lib/jvm

sudo tar -zxvf jdk-8u251-linux-x64.tar.gz -C /usr/lib/jvm/

sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk1.8.0_251/bin/java 1



Additional Notes:

openjdk by default does not contain JavaFX.

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