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<!--#set var="banner" value="Artemis - Chado : Database Loading"-->
<!--#include virtual="/perl/header"-->
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 <a href="http://gmod.org">
gmod.org</a>.
<ol>
<li><b>Download and Install Postgres.</b>
<pre>
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
</pre>
</li>
<li><b>Download and Install Chado.</b> See also the <a href="http://gmod.org/wiki/Chado">
Chado documentation</a>.
<pre>
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
</pre>
</li>
<li><b>Examples of Loading Sequences into the Database.</b>
<p><b>NC_001142:</b><p>
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).
<pre>
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
</pre>
<p><b>NC_008783:</b>
<p>
Add this to the organism table:
<pre>
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
</pre>
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:
<pre>
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';
</pre>
</li>
<li><b>Run Artemis.</b>
<pre>
./art -Dchado="localhost:2432/test?tim" -Dibatis \
-Djdbc.drivers=org.postgresql.Driver
</pre>
<p>If this is successful then the login window will appear and the
database manager will then open:</p>
<img src="databasemanager_example.gif" align="middle" alt="databasemanager_example"/>
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