GATK for gVCF compilation issue

Question

[win]

I want to generate a gVCF file using Google tools and in order to use that a modified version of GATK has to be used. That version can obtained from here: https://github.com/ctsa/gatk/zipball/gvcf

When I ran sudo ant from the directory where I unzipped the above file, I got the following errors:

[javac] Compiling 634 source files to /home/sqwork/ctsa-gatk-1017a93/build/java/classes

    [javac] /home/sqwork/ctsa-gatk-1017a93/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java:332: error: no suitable method found for join(isPhased()[...]RATOR,ignoreRefS[...]s())))
    [javac]         return ParsingUtils.join(isPhased() ? PHASED_ALLELE_SEPARATOR : UNPHASED_ALLELE_SEPARATOR,
    [javac]                            ^
    [javac]     method ParsingUtils.<T>join(String,Collection<T>) is not applicable
    [javac]       (inferred type does not conform to equality constraint(s)
    [javac]         inferred: Allele
    [javac]         equality constraints(s): Allele,String)
    [javac]     method ParsingUtils.join(String,String[]) is not applicable
    [javac]       (argument mismatch; bad type in conditional expression
    [javac]           List<String> cannot be converted to String[])
    [javac]   where T is a type-variable:
    [javac]     T extends Object declared in method <T>join(String,Collection<T>)
    [javac] /home/sqwork/ctsa-gatk-1017a93/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java:98: error: no suitable method found for add(Object)
    [javac]             annotations.add(pluginManager.createByType(c));
    [javac]                        ^
    [javac]     method Collection.add(T) is not applicable
    [javac]       (argument mismatch; Object cannot be converted to T)
    [javac]     method List.add(T) is not applicable
    [javac]       (argument mismatch; Object cannot be converted to T)
    [javac]   where T is a type-variable:
    [javac]     T extends Object declared in method <T>createAnnotations(PluginManager<T>,List<String>,List<String>)
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] Note: Some messages have been simplified; recompile with -Xdiags:verbose to get full output
    [javac] 2 errors

I have installed the correct version of JAVA v1.8 and am running it on Ubuntu 14.

Any ideas what might be wrong?

[Pierre Lindenbaum]

Please check ant REALLY uses java 1.8 using ant -d (look at the first lines... )

[win]

I am getting all sorts of Scala errors...seems like something in scala.compile. Do I have to have a scala compiler installed and where can it be found for Ubuntu 14

Answer 1

[win]

I think the issue was related to Java version. After I switched to v 1.7, the compilation was successful.