On 17/10/2018 10:19, Olivier Sallou wrote: > [...] > new IGV needs Java 9 or above. > The problem is Java 8 to 9 introduced some breaking changes with modules > support.
Hi, Olivier. The default under Ubuntu-MATE 18.04 LTS is Java 10: > /usr/lib/jvm/java-11-openjdk-amd64/bin/java -version > openjdk version "10.0.2" 2018-07-17 > OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2) > OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2, mixed mode) However, IGV did not work with Java 10 because of the missing classes. I forced it to Java 8 because that is what the IGV docs said was required: > http://software.broadinstitute.org/software/igv/ReleaseNotes/2.4.x "Java 8 is now required. IGV 2.4 requires Java version 8 to run" > /usr/lib/jvm/java-8-openjdk-amd64/bin/java -version > openjdk version "1.8.0_181" > OpenJDK Runtime Environment (build 1.8.0_181-8u181-b13-0ubuntu0.18.04.1-b13) > OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode) That also did not work because of the missing classes, so I patched it. > For igv (and others), command line is impacted, for example: > > Java8: java -cp ... ivg.jar > Java9: java --add-modules java.xml.bind -cp .. igv.jar > > as Java > 9 is default now, we package apps to be Java 9 compliant, not > Java 8 anymore > > in progress (not uploaded) igv packaging *should* be ok, but needs testing That's a problem for Bio-Linux 9 / Ubuntu 18.04 LTS, because the default is now Java 10 and the only other Java in the standard repo's is Java 8. > apt list '*jdk*jre*' > Listing... Done > openjdk-11-jre/bionic-updates,bionic-security,now 10.0.2+13-1ubuntu0.18.04.2 > amd64 [installed,automatic] > openjdk-11-jre-headless/bionic-updates,bionic-security,now > 10.0.2+13-1ubuntu0.18.04.2 amd64 [installed,automatic] > openjdk-11-jre-zero/bionic-updates,bionic-security 10.0.2+13-1ubuntu0.18.04.2 > amd64 > openjdk-8-jre/bionic-updates,bionic-security,now 8u181-b13-0ubuntu0.18.04.1 > amd64 [installed,automatic] > openjdk-8-jre-dcevm/bionic 8u112-2 amd64 > openjdk-8-jre-headless/bionic-updates,bionic-security,now > 8u181-b13-0ubuntu0.18.04.1 amd64 [installed,automatic] > openjdk-8-jre-zero/bionic-updates,bionic-security 8u181-b13-0ubuntu0.18.04.1 > amd64 The stand-alone version of IGV 2.4.14 does not work with Java 10: > /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xmx2000m > -Dapple.laf.useScreenMenuBar=true -Djava.net.preferIPv4Stack=true -jar > /usr/local/IGV/lib/igv.jar > WARN [2018-10-17T10:57:48,211] [Globals.java:138] [AWT-EventQueue-0] > Development mode is enabled > Detected an unsupported Java version. Java 8 is required by this release. I've not tried it with Java 9. HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.tra...@minke-informatics.co.uk
