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