diff --git a/docs/chado/databasemanager_example.gif b/docs/chado/databasemanager_example.gif new file mode 100644 index 0000000000000000000000000000000000000000..02264cf986ef0328d6ff884a904ac6d77eff7b2b Binary files /dev/null and b/docs/chado/databasemanager_example.gif differ diff --git a/docs/chado/dbloading.shtml b/docs/chado/dbloading.shtml new file mode 100644 index 0000000000000000000000000000000000000000..4093c8e9adc9d950f3e152263c5d2b4d56d768b0 --- /dev/null +++ b/docs/chado/dbloading.shtml @@ -0,0 +1,92 @@ +<!--#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"/> + diff --git a/docs/chado/index.shtml b/docs/chado/index.shtml index 25ae1a2858cc3faf04046c4a30738a2d187387f8..bf24b963a0998e71cdddbdd140745811db7f72fd 100644 --- a/docs/chado/index.shtml +++ b/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>