Upgrade instructions are only necessary when upgrading from an existing Tripal site to a later version. If you are following this User's Guide step-by-step for setup of a new Tripal site then you may skip the upgrade section.
Backup your current Drupal Site
Backup Database Files
Before begining any upgrade it is best practice to ensure you have a backup in the event something goes wrong. The upgrade process will cause major changes to the Drupal database tables but should not affect tables in Chado. If you installed Chado via Tripal then your backup will contain both the Drupal and Chado tables. The following command is one example for creating a backup using the pg_dump command of PostgreSQL:
pg_dump --no-owner -h [host] -U [user] -W -f [database].sql [database]
- [host] is the name of the server where the database resides
- [user] is the username used to log into PostgreSQL
- [database] the name of the database.
The resulting file will contain a set of SQL commands that if replayed will completely restore the database. In the event you need to restore the database you must recreate the database and then reload the data:
psql -U [user] -h [host] -d [database] -f [database].sql
Backup Data Files
Be sure to create a back up of your Drupal installation directory.
Information about Drush
These instructions make use of the 'drush' utility which provides a command-line interface for Drupal. If you do not have drush, the 7.x-5.9 version is available here: https://drupal.org/node/1973176. On some linux systems you can install drush using the native package management system. For example, on ubuntu you can install drush with the following command:
apt-get install drush
Drush commands shown below must always be executed inside the Drupal installation directory.