chado
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
chado [2010/01/13 09:07] – 172.26.15.184 | chado [2010/05/22 14:19] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 1: | Line 1: | ||
====== Chado ====== | ====== Chado ====== | ||
- | createdb --template=chado tparvadb | + | 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 |
- | psql chado | + | Convert file to gff using script: |
- | chado> SELECT * FROM organism; | + | <code> bp_genbank2gff3.pl NC_001142.gbk</ |
- | | + | |
- | chado> \q | + | |
+ | Create pgsql database. | ||
+ | |||
+ | |||
+ | < | ||
+ | psql tparvadb | ||
+ | chado> SELECT * FROM organism; | ||
+ | chado> INSERT INTO organism ( abbreviation, | ||
+ | |||
+ | chado> \q</ | ||
+ | |||
+ | Load gff3 data into database | ||
+ | < | ||
+ | |||
+ | Install Gbrowse2 | ||
+ | |||
+ | < | ||
+ | Directory for GBrowse' | ||
+ | Directory for GBrowse' | ||
+ | Directory for GBrowse' | ||
+ | Directory for GBrowse' | ||
+ | Directory for GBrowse' | ||
+ | Internet port to run demo web site on (for demo)? [8000] | ||
+ | Apache loadable module directory (for demo)? [/ | ||
+ | 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? | ||
+ | </ |
chado.1263373664.txt.gz · Last modified: 2010/05/22 14:19 (external edit)