bellerbrock · March 17, 2021 20:51
diff --git a/Ontology Update example b/Ontology Update example
 # Start by cloning  or pulling the latest updates in the ibp-sweetpotato-traits and Chado repos
 git clone https://github.com/Planteome/ibp-sweetpotato-traits.git
 git clone https://github.com/GMOD/Chado.git

 # Load the ontology terms, then update cvterm paths. It may be necessary to add to Chado modules to perl5lib: export PERL5LIB=/home/production/cxgn/Chado/chado/lib:$PERL5LIB
 perl Chado/chado/bin/gmod_load_cvterms.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -s CO_331 -d Pg -r postgres -p <PASSWORD> -n SweetpotatoTrait -u -v ibp-sweetpotato-traits/sweetpotato_trait.obo
 perl Chado/chado/bin/gmod_make_cvtermpath.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -d Pg -u postgres -p <PASSWORD> -c SweetpotatoTrait


 # Example for other ontologies
 perl Chado/chado/bin/gmod_load_cvterms.pl -H breedbase_db -D breedbase -s SGNSTAT -d Pg -r postgres -p postgres -n SGNStatistics_ontology -u -v sgn/ontology/cxgn_statistics.obo
	# Start by cloning or pulling the latest updates in the ibp-sweetpotato-traits and Chado repos
	git clone https://github.com/Planteome/ibp-sweetpotato-traits.git
	git clone https://github.com/GMOD/Chado.git

	# Load the ontology terms, then update cvterm paths. It may be necessary to add to Chado modules to perl5lib: export PERL5LIB=/home/production/cxgn/Chado/chado/lib:$PERL5LIB
	perl Chado/chado/bin/gmod_load_cvterms.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -s CO_331 -d Pg -r postgres -p <PASSWORD> -n SweetpotatoTrait -u -v ibp-sweetpotato-traits/sweetpotato_trait.obo
	perl Chado/chado/bin/gmod_make_cvtermpath.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -d Pg -u postgres -p <PASSWORD> -c SweetpotatoTrait


	# Example for other ontologies
	perl Chado/chado/bin/gmod_load_cvterms.pl -H breedbase_db -D breedbase -s SGNSTAT -d Pg -r postgres -p postgres -n SGNStatistics_ontology -u -v sgn/ontology/cxgn_statistics.obo