Thanks! I decided to install a local instance of Galaxy. The installation went fine, but now 
<div class="gmail_quote">I&#39;m not sure how to add a custom genome. I found some information in past comments on the user list but I&#39;m not sure I understand everything. All I&#39;ve got is a fasta file with all my supercontigs and a gtf file with the predicted models.</div>

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<div class="gmail_quote">And a somewhat basic question: am I supposed to be able to log in a local instance? It doesn&#39;t recognize my username and password, which I guess is normal since it is local, so what should I do?</div>

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<div class="gmail_quote">Cheers,</div>
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<div class="gmail_quote">David</div>
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<div class="gmail_quote">2011/8/26 Jennifer Jackson <span dir="ltr">&lt;<a href="mailto:jen@bx.psu.edu">jen@bx.psu.edu</a>&gt;</span><br></div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">===&gt;  Please use &quot;Reply All&quot; when responding to this email!&lt;===<br><br>Hello David,<br><br>
You are correct, this tool will only function when a database is defined with Galaxy already. This will include databases from UCSC and other sources and it sounds like you have already checked using the &quot;Edit Attributes&quot; form (pencil icon).<br>
<br>Using a custom genome currently would require a local instance where you could add you own genomes to the list of available databases.<br><a href="http://getgalaxy.org/" target="_blank">http://getgalaxy.org</a><br><br>
This may be a requirement that could be changed (ability to leave database as unassigned). I opened a request ticket that you can follow to see the review result for this proposal:<br><a href="https://bitbucket.org/galaxy/galaxy-central/issue/649/modify-aachanges-tool-to-allow-undefined" target="_blank">https://bitbucket.org/galaxy/<u></u>galaxy-central/issue/649/<u></u>modify-aachanges-tool-to-<u></u>allow-undefined</a><br>
<br>Thanks for sending in the suggestion!<br><br>Best,<br><br>Jen<br>Galaxy team<br><br><br>On 8/25/11 3:51 PM, David Joly wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>Hi everybody,<br>Maybe a dumb question but does someone know if we can use the aaChanges<br>tool on a custom genome? I have my SNP dataset and my gene dataset but I<br>
can only assign them to one of the genome build already in UCSC... I am<br>using the web server of galaxy. Do I need to install my own local<br>instance of Galaxy in order to add a custom genome build?<br>Thanks,<br>David<br>
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