Hi Thomas, <div>It turns out you discovered a bug in the cloud setup. We&#39;re missing a 2bit file and a respective reference to the file for the extract genomic DNA tool. We&#39;ll update the deployment but in the mean time you can configure the instance yourself with just a few commands:</div>

<div># connect to the instance</div><div>[local] $ ssh -i &lt;AWS private key file&gt; ubuntu@&lt;instance public IP&gt;</div><div># Become galaxy user</div><div>[ec2] $ sudo su galaxy</div><div># Change to the data dir and create 2bit file</div>

<div>[ec2] $ cd /mnt/galaxyIndices/genomes/Hsapiens/hg18/seq; faToTwoBit hg18.fa hg18.2bit</div><div># Update respective .loc file: </div><div>[ec2]: vi /mnt/galaxyTools/galaxy-central/tool-data/alignseq.loc</div><div># add this line at the bottom (use TAB to separate the 3 columns)</div>

<div>seq     hg18    /mnt/galaxyIndices/genomes/Hsapiens/hg18/seq/hg18.2bit<br><br></div><div>That should do it. </div><div>Let us know if you have any more trouble and we&#39;ll fix this issue when we release a new version of the deployment.</div>

<div><br></div><div>Enis</div><div><br></div><div><br><div class="gmail_quote">On Fri, Apr 15, 2011 at 11:55 AM, Randall, Thomas (NIH/NIEHS) [C] <span dir="ltr">&lt;<a href="mailto:thomas.randall@nih.gov">thomas.randall@nih.gov</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal">I set up a galaxy instance on the cloud, but got the following error when trying to convert a bed file of hg18 coordinates to fasta sequence with the “Extract Genomic DNA” tool as a test of the functionality of this instance:</p>

<p class="MsoNormal"><i>No sequences are available for &#39;hg18&#39;, request them by reporting this error.</i></p><p class="MsoNormal"><i> </i></p><p class="MsoNormal">Where did I go wrong? Likely I would get a similar error for other databases and indexes I might need and the instructions on the bitbucket site does not cover this (<a href="https://bitbucket.org/galaxy/galaxy-central/wiki/cloud" target="_blank">https://bitbucket.org/galaxy/galaxy-central/wiki/cloud</a>).</p>

<p class="MsoNormal">Otherwise this is a very nice setup.</p><p class="MsoNormal"> </p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas">Thomas Randall, PhD</span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas">Bioinformatics Scientist, Contractor</span></p>

<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas">National Institute of Environmental Health Sciences</span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas">P.O. Box 12233, Research Triangle Park, NC 27709</span></p>

<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas"><a href="mailto:randallta2@niehs.nih.gov" target="_blank">randallta2@niehs.nih.gov</a></span></p><p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas"><a href="tel:919-541-2271" value="+19195412271" target="_blank">919-541-2271</a></span></p>

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