[Gmod-help] Loading new organisms into Chado

[Barry Dancis]

Hi --

 I am trying to learn the Bulk files processing methods(http://gmod.org/wiki/GMODTools_TestCase) but when I ran the upload on the converted file into my exisitng Chado db  
 
 perl $lbin/gmod_bulk_load_gff3.pl -gfffile gff3/EU852811.gbk.gff -organism fromdata -dbname Chado -debug >& gmod-load.log  
 
  I got the following errors from in my log file:  
 
Preparing data for inserting into the Chado database  
(This may take a while ...)  
Organism Bio::Annotation::SimpleValue=HASH(0xa37a7d8) from data  
DBD::Pg::st fetchrow_array failed: no statement executing at /usr/local/share/pe  
rl/5.10.0/Bio/GMOD/DB/Adapter.pm line 1112, <GEN0> line 7.  
Bio::Annotation::SimpleValue=HASH(0xa37a7d8) organism not found in the database  
at /usr/local/bin/gmod_bulk_load_gff3.pl line 711, <GEN0> line 7.  
Issuing rollback() for database handle being DESTROY'd without explicit disconne  
ct() at /usr/local/bin/gmod_bulk_load_gff3.pl line 711.  
 
  The top of the original genbank file is  
LOCUS       EU852811               70578 bp    DNA     circular PLN 05-MAR-2009  
DEFINITION  Saccharomyces pastorianus Weihenstephan 34/70 mitochondrion,  
            complete genome.  
ACCESSION   EU852811  
 
and the organism is not one of the 12 that got loaded in the organism table during the installation of the Chado db.  
 
Is there a separate source for allowable organisms or should the bulk loader be able to load organisms not in the organism table?  
 
Looking at the GBrowse Configuration HOWTO document(http://gmod.org/wiki/GBrowse_Configuration_HOWTO) it describes the use of bp_bulk_load_gff.pl for creating databases from scratch, but when I run  
 
 perl $lbin/bp_bulk_load_gff3.pl -gfffile gff3/EU852811.gbk.gff -organism fromdata -dbname Chado -user postgres -passwd postgres -debug >& gmod-load.log  
 
I get  
 
Can't open perl script "/usr/local/bin/bp_bulk_load_gff3.pl": No such file or directory  
 
and I can't find the file in either the GMODTools tree or the GMOD installation kit.  
 
What is the diff betw gmod_bulk_load_gff3.pl and bp_bulk_load_gff3.pl? Do  they have diff purposes?  
 
Thanks,  
 
Barry

ps I also posted this on http://osdir.com/ml/science.biology.gmod.devel/2008-02/msg00000.html but I got no reply so I am posting it again here.