Re: [Fwd: [Gusdev-gusdev] dbest.pm plugin]

[Deborah F. P. <pi...@pc...>]

Hi Sucheta,

I use the dbEST plugin frequently. We have made a few changes in the
plugin lately so you may want to update it from cvs. The changes all 
relate to the option --taxon_id being changed to taxon_id_list which now 
takes a string (a comma delimited list of taxons) rather than an int (a 
single taxon_id). 

We maintain a mirrored dbEST database and this plugin was created to load 
data into GUS from our copy of the dbEST db. I didn't write the plugin and 
have never used the --update_file option, but I think it would be a list 
of id_est's that identify ests in the dbEST mirror that need to be updated 
but not a list of records that can be loaded directly into GUS.

One other point, I don't think you should use = between an option and a 
value. I believe that may be why it is hanging. 

                                                     Debbie






On Thu, 22 Apr 2004, Steve Fischer wrote:

> 
> 
> -------- Original Message --------
> Subject: 	[Gusdev-gusdev] dbest.pm plugin
> Date: 	Wed, 21 Apr 2004 18:48:32 -0400 (EDT)
> From: 	Sucheta Tripathy <su...@vb...>
> To: 	gus...@li...
> 
> 
> 
> Hi,
> 
> has anyone used dbest plugin. I have been trying to upload data with
> sequence files in genbank format using the following parameter, but it
> keeps hanging.
> 
> ga GUS::Common::Plugin::dbEST  --debug --fullupdate
> --log=/home/apps/oracle/data
> _load_dbest.log  --restart_number=1 --sqlVerbose --taxon_id=143371 
> --update_fil
> e=/usr/local/src/gus-related/dbest/tmp >& /home/apps/oracle/gusdev/dbest_err1
> 
> Any suggestion what file type I should be using etc..
> 
> Thanks
> 
> Sucheta
> 
>