Hi, A follow up to my own question. When I setup up the Galaxy instance from Cloudman the GATK tools were not included automatically. Something most have gone wrong during the upgrade process from Mercurial. Based on Dan Blankenberg's advice, I was able to got the GATK tools to show up in Galaxy by doing some hand editing of configuration files. But I have no reference genome. Should the reference genome been part of the initial installation if it had gone cleanly? Or including any reference genome for GATK tools supposed to be a manual post-installation process. Either way, I would be appreciative of pointers on how I can include the reference genomes for the GATK tools in Galaxy. Thanks Marco On Mon, Jul 8, 2013 at 12:43 PM, Marco Ocana <mocana(a)broadinstitute.org&gt;wrote: