[ensembl-dev] Inserting a new species in Ensembl

[Diogo Costa]

Hi,

I finally had the time to analyze the D. virilis database from Metazoa.

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.

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!

What I am doing wrong? :(

Diogo


On Thu, Oct 27, 2011 at 8:54 PM, Diogo Costa <costa.h4evr at gmail.com> wrote:

> 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
>> > _______________________________________________
>> > Dev mailing list    Dev at ensembl.org
>> > List admin (including subscribe/unsubscribe):
>> http://lists.ensembl.org/mailman/listinfo/dev
>> > Ensembl Blog: http://www.ensembl.info/
>>
>>
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