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.



On Mon, Jul 8, 2013 at 12:43 PM, Marco Ocana <moc...@broadinstitute.org>wrote:

> Hi,
> I am running an instance of Galaxy that I setup using Cloudman.
> We are trying to use the GATK Unified Genotyper, but we are missing the
> reference genomes.
> I saw in your website instructions on how to setup reference genomes for
> some other tools, but not for the Unified Genotyper.
> Where can I find instructions on how to setup reference genomes for this
> tool?
> Thanks
> Marco
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