Brute force - modencode migration

From WormBaseWiki
Revision as of 14:53, 7 April 2010 by Acabunoc (talk | contribs)
Jump to navigationJump to search

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. Only needed for wiggle data, skip to 2) 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';

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