I'm trying to install mutect, and as directed in the README.md, I've git cloned gatk-protected and tried to do 'mvn -Ddisable.queue install'. But I get the following issue. I've java 1.7 and maven 3.3.3. I followed the readme file present here. Could anyone please help in resolving the issue? Answer The README.md for mutect instructs to git reset --hard 3.1

MuTect install: GATK-protected: maven: Java-compile-error

I’m trying to install mutect, and as directed in the README.md, I’ve git cloned gatk-protected and tried to do ‘mvn -Ddisable.queue install’. But I get the following issue. I’ve java 1.7 and maven 3.3.3.

     1.[INFO] -------------------------------------------------------------
     2.[ERROR] COMPILATION ERROR :
     3.[INFO] -------------------------------------------------------------
     4.[ERROR] /home/krb/.../annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
     5.method java.util.Collection.add(T) is not applicable
     6.  (argument mismatch; java.lang.Object cannot be converted to T)
     7.method java.util.List.add(T) is not applicable
     8.  (argument mismatch; java.lang.Object cannot be converted to T)
     9.[INFO] 1 error
    10.[INFO] -------------------------------------------------------------
    11.[INFO] ------------------------------------------------------------------------ 
    12.[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (compile-java) on project gatk-framework: Compilation failure
    13.[ERROR] /home/krb/.../annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    14.[ERROR] method java.util.Collection.add(T) is not applicable
    15.[ERROR] (argument mismatch; java.lang.Object cannot be converted to T)
    16.[ERROR] method java.util.List.add(T) is not applicable
    17.[ERROR] (argument mismatch; java.lang.Object cannot be converted to T)
    18.[ERROR] -> [Help 1]
    19.org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (compile-java) on project gatk-framework: Compilation failure
    20./home/krb/.../annotator/interfaces/AnnotationInterfaceManager.java:[129,24] no suitable method found for add(java.lang.Object)
    21.method java.util.Collection.add(T) is not applicable
    22. (argument mismatch; java.lang.Object cannot be converted to T)
    23.method java.util.List.add(T) is not applicable
    24.  (argument mismatch; java.lang.Object cannot be converted to T)

I followed the readme file present here. Could anyone please help in resolving the issue?

Answer

The README.md for mutect instructs to git reset --hard 3.1 in the gatk-protected folder. I undid this action, which, my guess is, resulted in the use of the latest GATK-protected version. So, after I undid that reset command using git reflog, the procedure resumed and the mutect jar file was also successfully built.

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Answer