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Todd Harris > Bio-GMOD > Bio::GMOD::Admin::Update



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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.


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

The generic new() method is provided by 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 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/ 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

 -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.

 -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.

 -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.


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


None reported.


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


Todd W. Harris <>.

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.

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