[ensembl-dev] Inserting a new species in Ensembl

Diogo Costa costa.h4evr at gmail.com
Thu Oct 27 10:38:46 BST 2011


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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