add db loading docs

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9937 ee4ac58c-ac51-4696-9907-e4b3aa274f04

docs/chado/dbloading.shtml

+<!--#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.
+
+<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"/>
+

docs/chado/index.shtml

@@ -16,7 +16,8 @@
 	<ul>
 	<li><a href="overview.shtml">Overview Document</a></li>
 	<li><a href="admin.shtml">Admin Document</a></li>
-	<li><a href="storage.html">Data storage</a> (for the Pathogen Group)</li>
+	<li><a href="storage.html">Data Storage</a> (for the Pathogen Group)</li>
+	<li><a href="dbloading.shtml">Data Loading Examples</a></li>
 	</ul>
       
 <p>