NAME

auto_install_databases.pl - Download and install GFF data sets

SYNOPSYS

  % auto_install_databases.pl --rdms pg --user scott

DESCRIPTION

This program queries a web server to determine what data sets are available and presents the user with a list to choose from, with the option of getting several data sets at once. The chosen data sets are downloaded and they are used as inputs for the bulk loader of the specified relational database management system (either MySQL or PostgreSQL) to initialize and load the GFF and optionally fasta data.

NOTES

This program uses the bulk loader for its database (bp_bulk_load_gff.pl for mysql, bp_pg_bulk_load_gff.pl for postgres); read the documentation for those programs for caveats with their use.

Like the bulk loaders, this program uses \$TMPDIR to transiently store downloaded data, therefore, \$TMPDIR must have enough free space to store all of the raw data and the processed files for importation to the database.

To create your own web server data source, carefully copy the syntax and file structure of the default data source, as this program is very inflexible with regard to the obtaining information from the web server.

Since the data is being downloaded uncompressed from web server, it may take a very long time for the download and database load to complete. An hour or more is not out of the question for a large data set like wormbase.

COMMAND-LINE OPTIONS

Options can be abbreviated. For example, you can use -s for --server.

    --server           URL of web server to obtain datasets
                         Default = 'http://brie4.cshl.org:8000/'
    --rdms             RDMS to use (mysql or pg (Postgres))
                         Default = 'mysql'
    --user             Username to log into database server as
                         Default = ''
    --password         Password associated with username
                         Default = ''

SEE ALSO

Bio::DB::GFF, bp_bulk_load_gff.pl, bp_pg_bulk_load_gff.pl

AUTHOR

Scott Cain, cain@cshl.org

Copyright (c) 2003 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.