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

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IGB Helper

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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

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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.

 

Solution:

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 https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html

 

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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