gmod_fetch_features.pl - gmod_update_installation.pl - Maintain a MOD installation
This script provides a convenient mechanism to maintain a MOD installation. It should be excecuted with super user privileges.
$ gmod_update_installation.pl [options]
The following options are generically available for any MOD (default values in parenthesis):
MOD: --mod One of WormBase, FlyBase, SGD, etc Versions: --sync_to [live || dev] Sync to the current live or development version (live) --force [boolean] Force an update to the live or development version as appropriate (false) --version Update to the provided version (the current live version) System paths: --tmp Full path to the temporary directory to hold downloads (/usr/local/gmod/tmp) Miscellaneous: --purge [boolean] Purge the tmp download folder following upgrade (false) --help Display this message
Due to the wide variety of installation paths and MOD structures, each MOD may offer specialized options. These can be provided as "--option_name OPTION" which will be passed directly to the Bio::GMOD::Update::"MOD" object's update() method. For example, a typical command to maintain a WormBase installation looks like:
% gmod_update_installation.pl --analyze_logs --mysql_path /usr/local/mysql/data
For a full description of all available system paths and update options for your particular MOD, see Bio::GMOD::Adaptor and GMOD::Adaptor::your_mod.
You may wish to run this script under cron to ensure that your installation is always up-to-date. For my personal installation of WormBase, I use the following settings:
0 2 * * * /usr/local/bin/gmod_update_installation.pl --sync_to dev
This will check for and install a new version if present at 2 AM in the morning.
I keep my installation in sync with the development version. You will want to use the more stable live version, which you can specify using "--sync_to live" or by simply leaving off the "--sync_to" option altogether.
A suggested crontab entry for a simple local installation is:
gmod_update_intallation.pl --sync_to live --purge 1
A suggested crontab entry for official WormBase mirror sites is:
gmod_update_intallation.pl --sync_to live --purge 1 --analyze_logs 1
Todd Harris <harris@cshl.edu>.
Copyright (c) 2003-2005 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
