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?
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.