Enis &amp; Brad,<br><br>   I will prepare a list of tools and indices that are used frequently here and we can discuss about the standard distribution at Boston.<br><br>See you guys there,<br>Martin<br><br><div class="gmail_quote">
On Thu, Jun 24, 2010 at 5:22 PM, Enis Afgan <span dir="ltr">&lt;<a href="mailto:eafgan@emory.edu">eafgan@emory.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Maybe it would be a good idea then if we made some sort of a &#39;standard distribution&#39; for desirable genomes and agreed on where they get put on an EBS volume to be able to piggyback off of each other?<div>Discussing it at the meeting sounds great...</div>


<div><br></div><div>See you then,</div><div>Enis</div><div><div></div><div class="h5"><div><div><br><div class="gmail_quote">On Thu, Jun 24, 2010 at 4:53 PM, Brad Chapman <span dir="ltr">&lt;<a href="mailto:chapmanb@50mail.com" target="_blank">chapmanb@50mail.com</a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Enis and Martin;<br>
<div><br>
&gt; &gt;    I am using Galaxy on the cloud and noticed that a genome index and few<br>
&gt; &gt; tools were missing. More specifically, I noticed that bwa cannot be aligned<br>
&gt; &gt; with hg18 and rmdup and view commands are not available in the SAMTools. Do<br>
&gt; &gt; you have any plans for adding these in the near future?<br>
<br>
</div><div>&gt; We don&#39;t have a definitive plan for adding the specific functionality you<br>
&gt; asked about to the cloud but now that you have requested it, we can<br>
&gt; definitely look into it. In the near future (i.e., next couple of weeks),<br>
<br>
</div>This weekend I did some work towards trying to help with this sort<br>
of thing. This is a publicly available EBS snapshot with several<br>
common genomes (including hg18) indexed for bwa,  bowtie, maq and<br>
twobit:<br>
<br>
snap-67446d0f<br>
<br>
This also includes a galaxy directory with the .loc files indexed<br>
appropriately if you mount it as /vol/galaxy on an Amazon share; to<br>
give you an idea of the automated approach I was hoping to take<br>
towards aligning it with Galaxy.<br>
<br>
There are also two new Cloud BioLinux AMIs that include bwa,<br>
bowtie, samtools and lots of other stuff:<br>
<br>
64bit: ami-d62cc4bf<br>
32bit: ami-5423cb3d<br>
<br>
Enis, I&#39;m planning to add other genomes based on what y&#39;all have on<br>
the public galaxy and am happy to have you guys using whatever is<br>
useful from this. I&#39;m hoping to write up docs and something more<br>
official and we can discuss in a couple of weeks in Boston,<br>
<font color="#888888"><br>
Brad<br>
</font></blockquote></div><br></div></div>
</div></div></blockquote></div><br>