Support JDK11

[adamjorr]

Bug Report

JDK8 is no longer available for the current stable Debian release (buster). Trying to run gatk with an OpenJDK11 install fails.

I anticipate a WONTFIX since this is dependency related, but I figured it would be good to let people know

Affected tool(s) or class(es)

GATKRead, probably others too

Affected version(s)

• Latest public release version [4.1.2.0]
• Latest master branch as of [didn't test]

Description

Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/hellbender/transformers/ReadTransformer. Method 'org.broadinstitute.hellbender.utils.read.GATKRead lambda$identity$d67512bf$1(org.broadinstitute.hellbender.utils.read.GATKRead)' at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
	at org.broadinstitute.hellbender.transformers.ReadTransformer.identity(ReadTransformer.java:30)
	at org.broadinstitute.hellbender.engine.GATKTool.makePreReadFilterTransformer(GATKTool.java:345)
	at org.broadinstitute.hellbender.engine.GATKTool.getTransformedReadStream(GATKTool.java:374)
	at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:93)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
	at org.broadinstitute.hellbender.Main.main(Main.java:291)

This error seems related to the JRE version. You can still install JDK8 manually but that's not ideal for many users.

Steps to reproduce

Run GATK on OpenJDK11

Expected behavior

Program runs :)

Actual behavior

Error

[droazen]

@adamjorr We'd like to support newer versions of Java, but have historically been held back by our Apache Spark dependency. We'll take another look at our dependency situation, however, and see if an upgrade is possible at this point.

[gokalpcelik]

AdoptOpenJDK offers a debian/ubuntu repository for those to install java 1.8. That may be used. Other than that AdoptOpenJDK 11.0.4 works flawlessly for me under Debian Buster unless it is a spark tool.

[lbergelson]

In good news, the spark mailing list announced that spark master builds and runs all tests on 11 now. So it looks like support for java 11 coming in spark 3.0. When that is is going to be release isn't clear though. We should start moving to support java 11 in advance of that so we're ready when it releases.

[droazen]

Closing -- superseded by #6671