These notes are intended only as a guide and describes an installation carried out on a MacOSX (10.5.6). For details on Chado installation see gmod.org.
  1. Download and Install Postgres. 
    Download postgresql-8.3.5.

./configure --prefix=/Users/tjc/gmod/pgsl --with-pgport=2432 --with-includes=/Developer
make
make install

cd /Users/tjc/gmod/pgsl
bin/initdb -D data/

Added the line to data/postgresql.conf:
listen_addresses = 'localhost'

bin/postmaster -D data &
bin/createuser --createdb tim
bin/createlang plpgsql template1
bin/createdb --port=2432 test
  2. Download and Install Chado. See also the Chado documentation. 
    Download stable release (gmod-1.0.tar.gz)
Install BioPerl (http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix)
Install go-perl http://search.cpan.org/~cmungall/go-perl/

Install Bundle::GMOD from cpan

setenv GMOD_ROOT /usr/local/gmod
setenv CHADO_DB_NAME test
setenv CHADO_DB_USERNAME tim
setenv CHADO_DB_PORT 2432

Chado installation:
perl Makefile.PL
make
sudo make install
make load_schema
make prepdb
make ontologies
  3. Examples of Loading Sequences into the Database.

    NC_001142:

    You may find the following loading fails and you need to insert 'processed_transcript' as a sequence ontology cvterm. Or change them to 'mature_transcript' in the gff file (e.g. sed s'|processed_transcript|mature_transcript|' NC_001142.gff). 

    cat NC_001142.gbk | perl /usr/local/bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout > NC_001142.gff
cat NC_001142.gff | perl /usr/local/bin/gmod_bulk_load_gff3.pl -dbname test -organism "Saccharomyces cerevisiae" -dbuser tim -dbport 2432 -dbpass dd -recreate_cache

    NC_008783:

    Add this to the organism table: 

    INSERT INTO organism
  (abbreviation, genus, species, common_name, organism_id) VALUES 
  ('B.bacilliformis', 'Bartonella', 'bacilliformis', 'BB', 8783);

cat NC_008783.gbk | perl /usr/local/bin/bp_genbank2gff3.pl -noCDS -in stdin -out stdout > NC_008783.gff
cat NC_008783.gff | perl /usr/local/bin/gmod_bulk_load_gff3.pl -dbname test -organism "BB" -dbuser tim -dbport 2432 -dbpass dd -recreate_cache
    Artemis does not (by default) look for sequences that are loaded as a 'region'. So change the sequence type of NC_001142 from region to a chromosome: 
    UPDATE feature SET 
 type_id=(select cvterm_id from cvterm where cv_id=(
         select cv_id from cv where name='sequence') and name='chromosome') 
WHERE uniquename='NC_008783';
  4. Run Artemis. 
    ./art -Dchado="localhost:2432/test?tim" -Dibatis \
      -Djdbc.drivers=org.postgresql.Driver

    If this is successful then the login window will appear and the database manager will then open:

    databasemanager_example