Re: IGV

[Tony Travis <tony.travis@minke-informatics.co.uk>]

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.travis@minke-informatics.co.uk