chado
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chado [2010/01/13 09:09] – 172.26.15.184 | chado [2010/01/14 09:17] – 172.26.15.184 | ||
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====== Chado ====== | ====== 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: | ||
+ | < | ||
- | '' | + | 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.txt · Last modified: 2010/05/22 14:19 by 127.0.0.1