any reason to compile GATK from source?

[Kotoro]

the page describes the precompiled jar as:
"A pre-built version of the GATK with basic tools"

does that mean we get anything more buiding it from source?

I attempted to build it from source but received the following compiler error


gatk.compile.public.source:
[javac] Compiling 738 source files to /UCHC/Everson/tools/src/broadgsa-gatk-c981d24/build/java/classes
[javac] /UCHC/Everson/tools/src/broadgsa-gatk-c981d24/public/java/src/org/broadinstitute/sting/utils/MathUtils.java:1103: error: name clash: sum(Collection<Integer>) and sum(Collection<Number>) have the same erasure
[javac] public static long sum(Collection<Integer> x) {
[javac] ^
[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] 1 error

[vdauwera]

Hi,
There are a few tools that are not included in the pre-built version. One example is gsalib, an R library that allows you to work with GATK report files. To get that you need to build GATK from source.

The GATK team has a GetSatisfaction forum where they answer user questions, I recommend you check it out.

[Karl Klammer]

Hi Kotoro,

I had the same problem (to build GATK-Queue), but switching java from jdk1.7 to 1.6 fixed that, just in case you do want to build from source.