UPDATE using daphnia-work test database,
located at $ARGOS_ROOT/daphnia-work on iubio computer.

Changes from daphnia-db-load1.notes

WORKED EXAMPLE using GMOD Chado database 
in Argos system for Daphnia genome project  
Don Gilbert, 15 Feb 2004

==========================================================


==========================================================
STEP 0 .... Initialize Argos/GMOD environment
==========================================================

#n for daphnia-work test database -- SET THESE BY HAND
 setenv ARGOS_SERVICE 'daphnia-work'
 setenv DAPHNIA_WORK_PGDATA "/bio/biodb/daphnia-work/indices/pgsql"

 setenv DEBUG 1
 
#n added daphnia-work/conf/gmod.conf with proper db settings 

#n added daphnia-work/bin/ with symbolic links to
  $ARGOS_ROOT/gmod/bin/

#n need to add everyone to postgresdb, or have common user account?
oat.% psql -l                                                                           
FATAL:  user "vsingan" does not exist
psql: FATAL:  user "vsingan" does not exist

#n use CHADO_DB_USERNAME/username gilbertd for now; set in conf/gmod.conf
oat.% psql -U gilbertd -l                                                                         List of databases
     Name     |  Owner   | Encoding  
--------------+----------+-----------
 chadoxA      | gilbertd | SQL_ASCII
 daphnia-work | gilbertd | SQL_ASCII
 template0    | gilbertd | SQL_ASCII
 template1    | gilbertd | SQL_ASCII
 testdb       | gilbertd | SQL_ASCII

==========================================================
STEP 1 .... Make daphnia Chado DB
==========================================================

/bio/biodb/daphnia-work

oat.% bin/gmod_init_db.pl --help
Argos::Config using ARGOS_SERVICE=daphnia-work
Argos::Config reading configs at /c7/iubio/biodb/gmod/conf 
Argos::Config reading configs at /c7/eugenes/daphnia/testdb/conf 
Unknown option: help
Usage:
  -dbname = daphnia-work      [required, database name to create]
  -location = /bio/biodb/daphnia-work/indices/pgsql      [optional, database storage location]
  -ontology = go,song,.. [optional, or 'all', in folders in /bio/biodb/gmod/data/ontologies/]
  -initsql = /bio/biodb/gmod/install/initialize.sql    [optional, initializing sql]
  -organism = fruitfly,Drosophila melanogaster 
        [ optional: 'common,genus species', repeat -org=xxx as needed ]

% bin/gmod_init_db.pl \
  -dbname daphnia-work \
  -org='waterflea,Daphnia pulex' \
  -org='waterflea,Daphnia magna' \
  -org='waterflea,Daphnia pulicaria' \
  -org='waterflea,Daphnia arenata' \
  -ontology=obo_rel,song

oat.% bin/gmod_load_newseq.pl -org="D.pulex" -in=data/cdna/cDNA1.fa  -type=cDNA_clone -idmake="WFcl"
  Argos::Config using ARGOS_SERVICE=daphnia_work
  Argos::Config reading configs at /c7/iubio/biodb/gmod/conf 
  Argos::Config reading configs at /c7/eugenes/daphnia/testdb/conf 
  Loading sequences to database.
  Chado::LoadDBI(Main,dbi:Pg:dbname=daphnia-work;port=7302;host=localhost,,passwd)
  Working with Daphnia pulex.
  .................................................. 50 WFcl0001545
  .................................................. 100 WFcl0001595
  .................................................. 150 WFcl0001645
  .................................................. 200 WFcl0001695
  .................................................. 250 WFcl0001745
  .................................................. 300 WFcl0001795
  .................................................. 350 WFcl0001845
  ...............................................
  397 sequences added
  0 duplicate sequences skipped
  Done

... loaded other data ...


oat.% bin/gmod_list_db.pl
Argos::Config using ARGOS_SERVICE=daphnia_work
Argos::Config reading configs at /c7/iubio/biodb/gmod/conf 
Argos::Config reading configs at /c7/eugenes/daphnia/testdb/conf 

Feature summary for Chado  database
============================================================
Chado::LoadDBI(Main,dbi:Pg:dbname=daphnia-work;port=7302;host=localhost,gilbertd,passwd)
Features by Chado::Organism  n=13
2823    Daphnia pulex/D.pulex/waterflea
1495    Daphnia pulicaria/D.pulicaria/waterflea
619     Daphnia arenata/D.arenata/waterflea
------------------------------------------------------------

Features by Chado::Pub  n=8
1495    data/CGBvntr.fa 1076639416 type=seq_file
397     data/cdna/cDNA1.fa 1075475331 type=seq_file
619     data/cdna/cDNA2.fa 1075475336 type=seq_file
343     data/est1.fa 1076639361 type=seq_file
619     data/est2.fa 1076639394 type=seq_file
858     data/microsat/microDNA.fa 1075475373 type=seq_file
606     data/microsat/microsats.fa 1075475397 type=seq_file
------------------------------------------------------------

Features by Chado::Cv Sequence Ontology, n=897
962     EST
2511    cDNA_clone
1464    microsatellite
------------------------------------------------------------


Public ID counter
ID_Tag  Last_ID Description
WFms    1464    id counter for microsatellite by bin/gmod_load_newseq.pl
WFes    962     id counter for EST by bin/gmod_load_newseq.pl
WFcl    2511    id counter for cDNA_clone by bin/gmod_load_newseq.pl
------------------------------------------------------------

Chado::Feature  total=4937
============================================================
Done