Bio::GMOD::Admin::Update - Generics methods for updating a Bio::GMOD installation
# Update your Bio::GMOD installation use Bio::GMOD::Admin::Update; my $mod = Bio::GMOD::Admin::Update->new(-mod => 'WormBase'); $mod->update(-version => 'WS136');
Bio::GMOD::Admin::Update contains subroutines that simplify the maintenance of a Bio::GMOD installation.
The generic new() method is provided by Bio::GMOD.pm. new() provides the ability to override system installation paths. If you have a default installation for your MOD of interest, this should not be necessary. You will not normally interact with Bio::GMOD::Admin::Update objects, but instead with Bio::GMOD::Admin::Update::"MOD" objects.
See Bio::GMOD.pm and Bio::GMOD::Adaptor::* for a full description of all default paths for your MOD of interest.
update() is a wrapper method that should be overriden by Bio::GMOD::Admin::Update::"MOD" update(). The update() method should execute all steps necessary for a basic installation, returing an array of all components installed.
See Bio::GMOD::Admin::Update::WormBase for an example subclass. See bin/gmod_update_installation-wormbase.pl for a more detailed script that relies on this subclass.
Generic mirroring of files or directories provided by the Bio::GMOD::Util::Mirror module. If no options are provided, they will be fetched from the MOD default values stored in Bio::GMOD::Adaptor::*
Options: -remote_path Relative to the ftp root, file or directory to mirror -local_path Full path to the local destination directory -is_optional Warn instead of dying on errors
Options: -tmp_path full path to a temporary download directory -sync_to site to synchronize to (live || dev)
Prepare the temporary directory for downloading. The temporary directory is supplied by Bio::GMOD::Adaptor::* or can be overridden by passing a "-tmp_path=" option. If provided with "-sync_to=[live|dev]", this method will prepare a temporary directory according at "$tmp_path/$version" of the appropriate live or development site.
Rsync the local software to a remote module. Options will be culled from the Adaptor::MOD unless specified.
Options: -module Name of the rsync module to sync to -exclude Array referene of items to exclude -install_root Local dsetination path
Check that a provided path has sufficient disk space for an install.
Options: -path Full path to inspect for space -required Amount of space required for an install -component Symbolic name of the component being installed (for logging)
Returns true if there is sufficient space; dies with an error message otherwise.
Companion method to check_disk_space. Returns an array consisting of the mount point and available space for the provided path.
Delete the contents of the temporary directory following an update. See Bio::GMOD::Admin::Update::* for how this method might affect you!
Todd W. Harris <email@example.com>.
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.