Difference between revisions of "Brute force - modencode migration"
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* look at worm.conf | * look at worm.conf | ||
− | + | = Copy Databases = | |
− | + | == 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 22: | Line 23: | ||
> exit | > exit | ||
− | + | == 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) | * Write up how to do get GFF files and load to db - (bp_bulk_loader) | ||
* GFF files located: gff/modencode/pi ... /gff3 | * GFF files located: gff/modencode/pi ... /gff3 | ||
− | + | = 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 | ||
These are sparse files and should be copied compressed | These are sparse files and should be copied compressed | ||
+ | |||
pack: | pack: | ||
tar -pczf ARCHIVE_NAME.tar.gz /browser_data/worm/wiggle_binaries/PI/ | tar -pczf ARCHIVE_NAME.tar.gz /browser_data/worm/wiggle_binaries/PI/ | ||
Line 36: | Line 39: | ||
tar -xvzf ARCHIVE_NAME.tar.gz | tar -xvzf ARCHIVE_NAME.tar.gz | ||
− | + | = 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 |
Revision as of 13:37, 14 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
Copy Databases
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
$ mysql -uroot -p > CREATE DATABASE database_name; > exit $ mysql -uroot -p database_name < database_dump.sql
- grant select privileges to 'nobody' on the new database
$ mysql -uroot -p > GRANT SELECT ON `database_name`.* TO 'nobody'@'localhost'; > exit
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
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
These are sparse files and should be copied compressed
pack:
tar -pczf ARCHIVE_NAME.tar.gz /browser_data/worm/wiggle_binaries/PI/
unpack:
tar -xvzf ARCHIVE_NAME.tar.gz
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