Difference between revisions of "Brute force - modencode migration"
From WormBaseWiki
Jump to navigationJump to search| Line 5: | Line 5: | ||
* look at worm.conf | * look at worm.conf | ||
| − | 1) Copy Databases | + | 1) Copy Databases |
| − | a) | + | a) Using mysqldump: The following instructions seem to cause errors with conflicting Storage versions in production (wb-www1) |
* 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 18: | Line 18: | ||
GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost'; | GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost'; | ||
| − | b) Copy Databases: | + | b) Copy Databases: maybe this way will stop the Storage version problem? |
| − | * Write up how to do get GFF files and load | + | * Write up how to do get GFF files and load to db - (bp_bulk_loader) |
| + | * GFF files located: gff/modencode/pi ... /gff3 | ||
2) Browser Data: | 2) Browser Data: | ||
| Line 31: | Line 32: | ||
** -> 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 | ||
| − | * in production (wb-www1), set remote renderer = localhost for all the [TRACKS] | + | * in production (wb-www1), set remote renderer = localhost for all the [TRACKS] *this doesn't seem to work - debug |
Revision as of 15:41, 12 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
a) Using mysqldump: The following instructions seem to cause errors with conflicting Storage versions in production (wb-www1)
- 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: maybe this way will stop the Storage version problem?
- Write up how to do get GFF files and load to db - (bp_bulk_loader)
- GFF files located: gff/modencode/pi ... /gff3
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] *this doesn't seem to work - debug
