Re: [Gmod-ajax] Information about how to build demo server (fly and human)

[Mitch S. <mit...@be...>]

On 09/18/2009 03:53 AM, Motokazu Ishikawa wrote:
> If you could provide information about how to build demo server (fly and
> human) on your web site, it will greatly help me to do my work.
> Especially, I want to see contents of each data files (gff, bed).
>    

This is a description of the fly part.  The human part is more 
complicated; it involved downloading BED files from UCSC's table browser 
and then processing them with flatfile-to-json.pl.

I downloaded the GFF files from flybase; this is the current release as 
of this writing:

ftp://ftp.flybase.net/releases/current/dmel_r5.21/gff/

I installed bioperl 1.6 and the JSON and JSON::XS modules from CPAN.

I loaded the gff files into a mysql database by going into the directory 
with the GFF files and running this command:

$ bp_seqfeature_load.pl --dsn=dbi:mysql:dmel_5_15 --adaptor=DBI::mysql 
--fast --create dmel-*

(my database was named dmel_5_15 because 5.15 was the latest release 
when I did this; you'll probably want to name yours something else)

I used this JBrowse config file:

http://jbrowse.org/code/jbrowse-master/docs/examples/config/Dmel.json

(you'll want to change the description and db_args to reflect your data)

I downloaded the JBrowse code and placed it where the HTTP server would 
serve it (in my case, under /var/www/html).  Then (from the jbrowse 
directory) I did this to prepare the sequence data:

$ bin/prepare-refseqs.pl --conf ~/Dmel.json --refs 2L,2R,3L,3R,4,X

(the config file was in my home directory; in general, you want this to 
be somewhere other than the jbrowse directory, because it contains 
information on how to access your database, which you usually want to 
keep secret)

Then, once prepare-refseqs.pl was finished, I ran this (also within the 
jbrowse directory):

$ bin/biodb-to-json.pl --conf ~/JBrowseConfig.js

Then I ran generate-names to make the features searchable:

$ bin/generate-names.pl

And that should be it.

Mitch