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Chado

Create new T.pava Chr1 Chado database from Chr1 Genbank file. Local version of Genbank file does not work. Downloaded new file from Genbank: NC_001142.gbk

Convert file to gff using script:

 bp_genbank2gff3.pl NC_001142.gbk

Create pgsql database.

createdb --template=chado tparvadb
psql tparvadb
chado> SELECT * FROM organism;
chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');

chado> \q

Load gff3 data into database

gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gbk.gff

Install Gbrowse2

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/etc/gbrowse2] 
Directory for GBrowse's static images & HTML files? [/var/www/gbrowse2] 
Directory for GBrowse's temporary data [/var/tmp/gbrowse2] 
Directory for GBrowse's example databases [/var/www/gbrowse2/databases] 
Directory for GBrowse's CGI script executables? [/usr/lib/cgi-bin/gb2] 
Internet port to run demo web site on (for demo)? [8000] 
Apache loadable module directory (for demo)? [/usr/lib/apache2/modules] 
User account under which Apache daemon runs? [www-data] 
Automatically update Apache config files to run GBrowse? [y] 
Automatically update system config files to run gbrowse-slave? [y] 
chado.txt · Last modified: 2010/05/22 17:19 (external edit)