Todd Harris > Bio-GMOD > gmod_update_installation.pl

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NAME ^

gmod_update_installation.pl - Maintain a MOD installation

USAGE ^

This script provides a convenient mechanism to maintain a MOD installation. It should be excecuted with super user privileges.

  $ gmod_update_installation.pl [options]

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.

Running under cron ^

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

SEE ALSO ^

Bio::GMOD, Bio::GMOD::Update

AUTHOR ^

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.

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