I am trying to install GATK2 on my instance of Galaxy. I have installed binaries, then wrappers you developed.
During first phase of testing, tools were complaining about JAVA_VAR_PATH being not properly set. I hard coded it in the .bashrc of my galaxyuser. I am not sure it is the best practice but at least tools seems to work.
To test the installation, I ran ReduceReads. I got an error message about the fact that it was deprecated
##### ERROR MESSAGE: Walker ReduceReads is no longer available in the GATK; it has been deprecated since version 3.0 (use recommended best practices pipeline with the HaplotypeCaller)
I was wondering what was the rational of having this wrapper around (backward reproducibility?). I guess I am doing something wrong...any thoughts.
Thanks for the great work,