Difference between revisions of "Brute force - modencode migration"
From WormBaseWiki
Jump to navigationJump to search| Line 3: | Line 3: | ||
* look at worm.conf | * look at worm.conf | ||
| − | Databases | + | 1) Copy Databases. Only needed for wiggle data, skip to 2) down for sam/bam: |
* 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 | ** mysqldump -uviewer -pviewer database_name > database_dump.sql | ||
| Line 14: | Line 14: | ||
*** GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost'; | *** GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost'; | ||
| − | Browser Data: | + | 2) Browser Data: |
* copy relevant browser_data (wiggle files/sambam) to the same location on wb-dev | * copy relevant browser_data (wiggle files/sambam) to the same location on wb-dev | ||
** /browser_data/worm/wiggle_binaries/PI_NAME | ** /browser_data/worm/wiggle_binaries/PI_NAME | ||
** /browser_data/worm/sam_binaries/PI_NAME | ** /browser_data/worm/sam_binaries/PI_NAME | ||
| − | Config: | + | 3) Config update: |
* copy relevant conf files to wb-dev | * copy relevant conf files to wb-dev | ||
** -> modencode: /var/www/conf/FOLDER_SPECIFIED_IN_WORM.CONF | ** -> modencode: /var/www/conf/FOLDER_SPECIFIED_IN_WORM.CONF | ||
** -> wb-dev : /usr/local/wormbase/gbrowse_current/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 | * look at worm.conf and copy the appropriate #include function and database definitions to c_elegans.conf | ||
Revision as of 14:21, 7 April 2010
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) down for sam/bam:
- 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';
- first create database database_name
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
