Hi,<div><br></div><div>A follow up to my own question.</div><div>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.</div>
<div>Based on Dan Blankenberg&#39;s advice, I was able to got the GATK tools to show up in Galaxy by doing some hand editing of configuration files.</div><div><br></div><div>But I have no reference genome.</div><div><br></div>
<div>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. </div><div>Either way, I would be appreciative of pointers on how I can include the reference genomes for the GATK tools in Galaxy.</div>
<div><br></div><div>Thanks</div><div><br></div><div>Marco</div><div><br><br><div class="gmail_quote">On Mon, Jul 8, 2013 at 12:43 PM, Marco Ocana <span dir="ltr">&lt;<a href="mailto:mocana@broadinstitute.org" target="_blank">mocana@broadinstitute.org</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<div><br></div><div>I am running an instance of Galaxy that I setup using Cloudman.</div><div>We are trying to use the GATK Unified Genotyper, but we are missing the reference genomes.</div>
<div>I saw in your website instructions on how to setup reference genomes for some other tools, but not for the Unified Genotyper.</div>
<div>Where can I find instructions on how to setup reference genomes for this tool?</div><div><br></div><div>Thanks</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Marco</div>
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