Expanding config variables such as $GATK_PATH and $PICARD_DIR, module system specific

Hi Brad,

I'm setting up the upstream pipeline in our HPC cluster. Since the location of picard and GATK varies among module system installations, we have to define $GATK_HOME and $PICARD_HOME in our `bcbio_system.yaml` config file Here's a little fix for that.

Cheers!
Roman

@mariogiov, @vezzi