Switch GATK and DISCVR-seq to use modern java version

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java

@@ -48,21 +48,6 @@ public void setMaxRamOverride(Integer maxRamOverride)
         _maxRamOverride = maxRamOverride;
     }
 
-    public void addJava8HomeToEnvironment()
-    {
-        //since GATK requires java8, set JAVA_HOME to match this:
-        File java8 = new File(SequencePipelineService.get().getJava8FilePath()).getParentFile();
-        if (java8.getParentFile() == null)
-        {
-            getLogger().debug("unexpected path to java8, cannot determine JAVA_HOME: " + java8.getPath());
-            return;
-        }
-
-        String javaDir = java8.getParentFile().getPath();
-        getLogger().debug("setting JAVA_HOME to java8 location: " + javaDir);
-        addToEnvironment("JAVA_HOME", javaDir);
-    }
-
     public boolean jarExists()
     {
         return getJAR(false) != null;
@@ -80,7 +65,7 @@ protected void ensureDictionary(File referenceFasta) throws PipelineJobException
     public String getVersionString() throws PipelineJobException
     {
         List<String> args = new ArrayList<>();
-        args.add(SequencePipelineService.get().getJava8FilePath());
+        args.add(SequencePipelineService.get().getJavaFilepath());
         args.addAll(SequencePipelineService.get().getJavaOpts(_maxRamOverride));
         args.add("-jar");
         args.add(getJAR().getPath());
@@ -102,7 +87,7 @@ protected String getPackageName()
     public List<String> getBaseArgs(@Nullable String toolName)
     {
         List<String> args = new ArrayList<>();
-        args.add(SequencePipelineService.get().getJava8FilePath());
+        args.add(SequencePipelineService.get().getJavaFilepath());
         args.addAll(SequencePipelineService.get().getJavaOpts(_maxRamOverride));
         args.add("-jar");
         args.add(getJAR().getPath());

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -972,8 +972,6 @@ private void prepareLuceneIndex(Logger log) throws PipelineJobException
         log.debug("Generating VCF full text index for file: " + getExpData().getFile().getName());
 
         DISCVRSeqRunner runner = new DISCVRSeqRunner(log);
-        runner.addJava8HomeToEnvironment();
-
         if (!runner.jarExists())
         {
             log.error("Unable to find DISCVRSeq.jar, skiping lucene index creation");