David, because of the restrictive licensing terms of GATK2 the main Galaxy Team will not continue to develop any GATK tools except for those which remain under the open source license (basically, GATK 1.6). We will be very happy to have wrappers for these and other non-open-source tools contributed to the toolshed however for those who wish to use them. -- jt On Tue, Sep 11, 2012 at 10:41 AM, David Hoover <hooverdm@helix.nih.gov> wrote:

Is anyone working on adapting the GATK tools for a more recent version of GATK? The distributed version is 1.4, and GATK is up to 2.1.