Hi,<div><br></div><div>I finally had the time to analyze the D. virilis database from Metazoa.</div><div><br></div><div>I have confirmed that some entries were missing from the meta table of my custom core database, but the specie still doesn't show in the Ensembl home page (species list). A blank space holder is shown instead: blank image and blank name.</div>
<div><br></div><div>In an attempt to pinpoint the problem, I imported the DB from Metazoa into MySQL and changed Drosophila_virilis.ini (custom ini) file to point to this database. This makes the entry show up correctly!</div>
<div><br></div><div>What I am doing wrong? :(</div><div><br></div><div>Diogo</div><div><div><br><br><div class="gmail_quote">On Thu, Oct 27, 2011 at 8:54 PM, Diogo Costa <span dir="ltr"><<a href="mailto:costa.h4evr@gmail.com">costa.h4evr@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Thank you, Karyn! I'll take a look at it and try to see what I am missing.<div><span class="HOEnZb"><font color="#888888">Diogo</font></span><div>
<div class="h5"><br><div><br>On Thursday, October 27, 2011, Karyn Megy wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Diogo,<br>
<br>
<br>
You can find an Ensembl database populated for "Drosophila virilis" on the Ensembl Genomes website<br>
(<a href="http://metazoa.ensembl.org/Drosophila_virilis/Info/Index/" target="_blank">http://metazoa.ensembl.org/Drosophila_virilis/Info/Index/</a>)<br>
<br>
The MySQL dump is here:<br>
<a href="ftp://ftp.ensemblgenomes.org/pub/metazoa/release-11/mysql/drosophila_virilis_core_11_64_12/" target="_blank">ftp://ftp.ensemblgenomes.org/pub/metazoa/release-11/mysql/drosophila_virilis_core_11_64_12/</a><br>
<br>
You could use this to make sure your tables are populated properly (or use these files directly). From experience, the meta and analysis_description tables contain lots of information required for proper web display.<br>
<br>
Cheers,<br>
Karyn.<br>
<br>
<br>
<br>
On 27 Oct 2011, at 10:38, Diogo Costa wrote:<br>
<br>
> Hello!<br>
><br>
> In the process of my masters dissertation I created a mirror of Ensembl web site in a local server. It is up and running except for BLAST and search functionality.<br>
><br>
> I've been trying to insert a new species (Drosophila virilis, from FlyBase), but have been unsuccessful so I was wondering if someone could give some pointers!<br>
><br>
> I've tried to follow the instructions on these two sites:<br>
><br>
> - Ensembl doc:<br>
> <a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-doc/loading_sequence_into_ensembl.txt?revision=1.5&root=ensembl&pathrev=MAIN" target="_blank">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-doc/loading_sequence_into_ensembl.txt?revision=1.5&root=ensembl&pathrev=MAIN</a><br>
><br>
> - Loading an Ensembl species database from scratch<br>
> <a href="http://www.warelab.org/blog/?p=218" target="_blank">http://www.warelab.org/blog/?p=218</a><br>
><br>
> I have the genome sequences by scaffold and chromossomes and the CDS in FASTA format. Following the "Loading chromosome sequences and faking the assembly" section of the second link, I adjusted the script given to suit my data. I've managed to insert the data into the MySQL database.<br>
><br>
> Then, I followed the instructions on <a href="http://www.ensembl.org/info/docs/webcode/species/index.html" target="_blank">http://www.ensembl.org/info/docs/webcode/species/index.html</a> to make the specie information available from the website.<br>
><br>
> However, the specie doesn't show up in the list of species (yes, I have deleted config/packed/* and config/config.packed and restarted the server).<br>
> When accessing the URL manually (http://..../Drosophila_virilis/Info/Index) I don't get any error in the log file.<br>
><br>
> The server is running on top of Fedora 14, if it makes any difference..<br>
><br>
> I don't really know what I can do, or what other information I need to give to Ensembl.<br>
><br>
> Is this not the way to go?<br>
><br>
> Sorry for the long email,<br>
> Diogo Costa<br>
> Portugal<br>
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<br>
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