NAME

Bio::GMOD::Update - Generics methods for updating a Bio::GMOD installation

SYNOPSIS

# Update your Bio::GMOD installation
use Bio::GMOD::Update;
my $mod = Bio::GMOD::Update->new(-mod => 'WormBase');
$mod->update(-version => 'WS136');

DESCRIPTION

Bio::GMOD::Update contains subroutines that simplify the maintenance of a Bio::GMOD installation.

PUBLIC METHODS

$mod = Bio::GMOD::Update->new()

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::Update objects, but instead with Bio::GMOD::Update::"MOD" objects.

See Bio::GMOD.pm and Bio::GMOD::Adaptor::* for a full description of all default paths for your MOD of interest.

$mod->update(@options)

update() is a wrapper method that should be overriden by Bio::GMOD::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::Update::WormBase for an example subclass. See bin/gmod_update_installation-wormbase.pl for a more detailed script that relies on this subclass.

$mod->mirror(@options);

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

$mod->prepare_tmp_dir(@options)

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.

$mod->rsync_software(@options);

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

$mod->check_disk_space(@options);

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.

$mod->get_available_space(-path => $path);

Companion method to check_disk_space. Returns an array consisting of the mount point and available space for the provided path.

$mod->cleanup()

Delete the contents of the temporary directory following an update. See Bio::GMOD::Update::* for how this method might affect you!

BUGS

None reported.

SEE ALSO

Bio::GMOD, Bio::GMOD::Util::CheckVersions

AUTHOR

Todd W. 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.