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: