Brute force - modencode migration

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