Breedbase configuration files

Configuration files specific for the LSU rice breeding program instance of Breedbase. Below are the commands needed to get the LSU breedbase instance up and running.

Start breedbase with docker-compose

docker-compose up -d

Enter breedbase_web

docker exec -it breedbase_web bash

Make a new database 'breedbase_fresh' in the the breedbase_db container

psql -U postgres -h breedbase_db -c "create database breedbase_fresh"

Delete old database 'breedbase' in the the breedbase_db container

psql -U postgres -h breedbase_db -c "drop database breedbase"

Add user "web_usr" and make password "postgres"

psql -U postgres -h breedbase_db -c "create user web_usr"
psql -U postgres -h breedbase_db -c "alter user web_usr password 'postgres'"

Fill 'breedbase_fresh' using fixture file

psql -U postgres -h breedbase_db -d breedbase_fresh -f t/data/fixture/empty_fixture.sql

Run patches on 'breedbase_fresh'

cd db
./run_all_patches.pl -u postgres -p postgres  -h breedbase_db -d breedbase_fresh -e janedoe

Load ontologies

perl ~/cxgn/Chado/chado/bin/gmod_load_cvterms.pl -H breedbase_db -D breedbase_fresh -d Pg -s LSU_01 -v -u -r postgres -n lsuRice -p postgres ~/cxgn/lsurice-breedbase/ontology/lsu_rice2.obo 

Delete defualt ontologies

psql -U postgres -h breedbase_db -d breedbase_fresh -c "delete from cvterm where cv_id = 16 or cv_id = 54 or cv_id = 58 or cv_id = 59 or cv_id = 4 or cv_id = 7 or cv_id =8 or cv_id = 9 or cv_id=10 or cv_id=13 or cv_id=14 or cv_id=19"
psql -U postgres -h breedbase_db -d breedbase_fresh -c "delete from cvprop where cv_id = 16 or cv_id=58 or cv_id=59 or cv_id=64"

Tag ontology as trait ontology

perl ~/cxgn/sgn/bin/load_composed_cvprops.pl -H breedbase_db -D breedbase_fresh -T lsuRice