Brute force - modencode migration
From WormBaseWiki
Jump to navigationJump to search
- 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
Databases stuff only needed for wiggle data, skip 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
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
Config:
- 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