chado
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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.1263461866.txt.gz · Last modified: 2010/05/22 14:19 (external edit)