[ensembl-dev] Inserting a new species in Ensembl

[Karyn Megy]

Hi Diogo, 


You can find an Ensembl database populated for "Drosophila virilis" on the Ensembl Genomes website 
(http://metazoa.ensembl.org/Drosophila_virilis/Info/Index/)

The MySQL dump is here: 
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-11/mysql/drosophila_virilis_core_11_64_12/

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.

Cheers,
Karyn.



On 27 Oct 2011, at 10:38, Diogo Costa wrote:

> Hello!
> 
> 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.
> 
> 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!
> 
> I've tried to follow the instructions on these two sites:
> 
> - Ensembl doc:
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-doc/loading_sequence_into_ensembl.txt?revision=1.5&root=ensembl&pathrev=MAIN
> 
> - Loading an Ensembl species database from scratch
> http://www.warelab.org/blog/?p=218
> 
> 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. 
> 
> Then, I followed the instructions on http://www.ensembl.org/info/docs/webcode/species/index.html to make the specie information available from the website.
> 
> 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).
> When accessing the URL manually (http://..../Drosophila_virilis/Info/Index) I don't get any error in the log file.
> 
> The server is running on top of Fedora 14, if it makes any difference..
> 
> I don't really know what I can do, or what other information I need to give to Ensembl.
> 
> Is this not the way to go? 
> 
> Sorry for the long email,
> Diogo Costa
> Portugal
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