Difference between revisions of "Brute force - modencode migration"
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a) Follow these steps if the perl module Storage is the same in both environments. If not, skip to b) | a) Follow these steps if the perl module Storage is the same in both environments. If not, skip to b) | ||
* dump databases using mysqldump (to find out which ones to get, look at conf files) | * dump databases using mysqldump (to find out which ones to get, look at conf files) | ||
| − | + | mysqldump -uviewer -pviewer database_name > database_dump.sql | |
* copy database_dump.sql files to wb-dev | * copy database_dump.sql files to wb-dev | ||
* import databases | * import databases | ||
** first create database database_name | ** first create database database_name | ||
| − | + | CREATE DATABASE database_name; (as root) | |
| − | + | mysql -uroot -p database_name < database_dump.sql | |
** grant select privileges to 'nobody' on the new database | ** grant select privileges to 'nobody' on the new database | ||
| − | + | GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost'; | |
b) Copy Databases: when Storage is different versions. | b) Copy Databases: when Storage is different versions. | ||
Revision as of 17:34, 9 April 2010
This method does not lift-over the data to the current version of WormBase. This data will be mapped to WS190. This a temporary fix while we wait for the data to get lifted over at Sanger.
Get account on modencode.oicr.on.ca (email helpdesk@oicr.on.ca with request) this is their gbrowse production server.
- Configuration files: /var/www/conf/
- look at worm.conf
1) Copy Databases. Only needed for wiggle data, skip to 2) for sam/bam:
a) Follow these steps if the perl module Storage is the same in both environments. If not, skip to b)
- dump databases using mysqldump (to find out which ones to get, look at conf files)
mysqldump -uviewer -pviewer database_name > database_dump.sql
- copy database_dump.sql files to wb-dev
- import databases
- first create database database_name
CREATE DATABASE database_name; (as root) mysql -uroot -p database_name < database_dump.sql
- grant select privileges to 'nobody' on the new database
GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost';
b) Copy Databases: when Storage is different versions.
- Write up how to do get GFF files and load
2) Browser Data:
- copy relevant browser_data (wiggle files/sambam) to the same location on wb-dev
- /browser_data/worm/wiggle_binaries/PI_NAME
- /browser_data/worm/sam_binaries/PI_NAME
3) Config update:
- copy relevant conf files to wb-dev
- -> modencode: /var/www/conf/FOLDER_SPECIFIED_IN_WORM.CONF
- -> wb-dev : /usr/local/wormbase/gbrowse_current/conf/FOLDER_SPECIFIED_IN_WORM.CONF
- look at worm.conf and copy the appropriate #include function and database definitions to c_elegans.conf
- in production (wb-www1), set remote renderer = localhost for all the [TRACKS]
