[ensembl-dev] Inserting a new species in Ensembl

[Diogo Costa]

Thank you, Karyn! I'll take a look at it and try to see what I am missing.
Diogo

On Thursday, October 27, 2011, Karyn Megy wrote:

> 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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>
>
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