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



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Bio::GMOD::Admin::Update::WormBase - Methods for updating a WormBase installation


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


Bio::GMOD::Admin::Update::WormBase contains subroutines that simplify the maintenance of a WormBase installation. You will not normally need to create a Bio::GMOD::Admin::Update::WormBase object manually - these will be created automatically by Bio::GMOD::Admin::Update.


$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 WormBase installation this should not be necessary. In particular, the following paths may differ on your system:

  --tmp_path    The full path to your temporary download directory
  --mysql_path  The full path to your mysql directory
  --acedb_path  The full path to your acedb directory

If these options are not provided, the installer will download files to /usr/local/gmod/tmp, install acedb files at /usr/local/acedb, and install GFF mysql databases at /usr/local/mysql/data.

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


update() is provided as convenience, wrapping individual methods for downloading prepackaged databases necessary for a MOD installation. Typically, update() is provided by the MOD adaptor of interest.

For the Bio::GMOD::Admin::Update::WormBase module, update() performs the following steps:

   - fetch a tarball of the acedb database
   - fetch tarballs of several MySQL GFF databases
   - fetch blast and blat database tarballs
   - unpack tarballs and adjust permissions
   - rsyncs software to the production server

Required options are:

 -version     The WS version to update to (if available on the server)

If you'd like to simply download but not install the prepackaged databases, you can pass boolean true using:

 -dl_only    download but not install

update() returns a list of all components succesfully downloaded (and installed) if succesful or false if an error occured. You can fetch the nature of the error by calling $mod->status

fetch_acedb, fetch_elegans_gff, fetch_briggsae_gff, fetch_blast

These four methods can all be used to fetch and install the four primary components of a WormBase installation as outlined above.

Like update(), you can specify the -version and -dl_only options as discussed above. This enables you to write scripts that download several different versions of the database for a single instance of WormBase::Update. You may also specify either acedb_path or mysql_path to specify the path to the acedb installation directory or the mysql data directory as appropriate instead of supplying it to the new() method.


Analyze WormBase logs for the previous version. You must specify the WS version of the previous version. This method requires that you have both Analog and Report Magic installed and that they exist in your path (or the superusers path). Large access logs can take some time to analyze. This option will also analyze logs on a year-to-date and server lifetime-to-date basis.


Delete the contents of the temporary directory. Due to the size of the prepackaged databases, this is not recommended unless all steps have succeeded!




None reported.


Bio::GMOD, Bio::GMOD::Admin::Update, Bio::GMOD::Adaptor


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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