Every time I try to run IGV, I'm greeted with can't find Java Runtime error dialog. I have Java installed on the system as running /usr/libexec/java_home returns /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home. I also have the JAVA_HOME variable set to the above value (though the value is not included in my PATH).

The java command is also accessible through command line so I don't see any reason why the application can't access it. Running java -version returns 1.8.0_05.

I believe I also have the legacy Apple Java 6 installed although the preference pane for that is not available (maybe something wrong here?) and I don't know how to verify its installation.

I'm on 10.13 High Sierra.

*** Update Running /usr/libexec/java_home -V shows that both Java 6 and 8 are installed:

Matching Java Virtual Machines (3):
    1.8.0_05, x86_64:   "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home
    1.6.0_65-b14-468, x86_64:   "Java SE 6" /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
    1.6.0_65-b14-468, i386: "Java SE 6" /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home


Any help is appreciated.

  • How exactly are you running Igv? – Mark Oct 22 '17 at 11:15
  • Also does IGV require a specific version of Java? – Steve Chambers Oct 22 '17 at 15:46
  • @Mark double clicking the .app downloaded from their website. – DarthPaghius Oct 22 '17 at 19:29
  • Clcicking on apps runs things from the Finder which does not look at any environment variables in the shell. What does IGV documentation say – Mark Oct 23 '17 at 12:23
  • @Mark It says drop the app somewhere and double click it. It probably looks for Java in some default directory which doesn't match the one on my system. – DarthPaghius Oct 23 '17 at 22:32

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