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 <mocana(a)broadinstitute.org>wrote:
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
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