Error installing IGV

[Jesse Huerta]

Howdy, I am trying to install IGV_Linux_2.17.3_WithJava with:

bash igv.sh and bash /opt/igv_hidpi.sh but both result in the same error about java

java -version
openjdk version "1.8.0_402"
OpenJDK Runtime Environment (build 1.8.0_402-b06)
OpenJDK 64-Bit Server VM (build 25.402-b06, mixed mode)

Error occurred during initialization of boot layer
java.lang.module.FindException: Module org.apache.logging.log4j.core not found, required by org.igv

Any ideas what this could be?

[igv-help]

This looks odd. The  2.17.3 distribution includes Java 17, not Java 8. In fact, IGV 2.17.3 will not run with Java 8.

When you run the igv.sh script it should tell you whether it found the bundled Java (ie will print out "Using bundled JDK.") or if it's using the Java installed on your system (ie will print out "Using system JDK.") Which did you see?

Where did you download it from? It may also be helpful to see the igv.sh script you are running and  a listing of the enclosing IGV_Linux_2.17.3 directory.

[Jesse Huerta]

I am downloading IGV for Linux from here: https://igv.org/doc/desktop/#DownloadPage/ 

The script I'm running is in that folder. Did you want me to paste that here?

[igv-help]

Sure

[Jesse Huerta]

 bash igv.sh
echo Using bundled JDK.
Unrecognized option: --module-path=/opt/IGV_Linux_2.16.0/lib
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

[Jesse Huerta]

 #!/bin/sh

#This script is intended for launch on *nix machines

#-Xmx8g indicates 8 gb of memory.
#To adjust this (or other Java options), edit the "$HOME/.igv/java_arguments"
#file.  For more info, see the README at
#https://raw.githubusercontent.com/igvteam/igv/master/scripts/readme.txt
#Add the flag -Ddevelopment = true to use features still in development
#Add the flag -Dsun.java2d.uiScale=2 for HiDPI displays
prefix=`dirname $(readlink -f $0 || echo $0)`

# Check whether or not to use the bundled JDK
if [ -d "${prefix}/jdk-11" ]; then
    echo echo "Using bundled JDK."
    JAVA_HOME="${prefix}/jdk-11"
    PATH=$JAVA_HOME/bin:$PATH
else
    echo "Using system JDK."

else
    echo "Using system JDK."
fi

# Check if there is a user-specified Java arguments file
if [ -e "$HOME/.igv/java_arguments" ]; then
    java -showversion --module-path="${prefix}/lib" -Xmx8g \
        @"${prefix}/igv.args" \
        -Dapple.laf.useScreenMenuBar=true \
        -Djava.net.preferIPv4Stack=true \
        -Djava.net.useSystemProxies=true \
        @"$HOME/.igv/java_arguments" \
        --module=org.igv/org.broad.igv.ui.Main "$@"
else
    java -showversion --module-path="${prefix}/lib" -Xmx8g \
        @"${prefix}/igv.args" \
        -Dapple.laf.useScreenMenuBar=true \
        -Djava.net.preferIPv4Stack=true \
        -Djava.net.useSystemProxies=true \

        -Djava.net.preferIPv4Stack=true \
        -Djava.net.useSystemProxies=true \
        --module=org.igv/org.broad.igv.ui.Main "$@"
fi

[igv-help]

That's not the 2.17.3 version of the script. Maybe an old version of the Download page is cached in your browser.

Here's a direct link to the zip file: https://data.broadinstitute.org/igv/projects/downloads/2.17/IGV_Linux_2.17.3_WithJava.zip

Please try that one.

[Jesse Huerta]

Thank you, I downloaded it again and removed it off my system. Now I am able to run it.

[igv-help]

Glad to hear it.