From Code to Community: Sponsoring The Perl and Raku Conference 2025 Learn more

AJPAGE / Bio-MLST-Check-2.1.1706216 / bin / download_mlst_databases 

            

              
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
—
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88

              
#!/usr/bin/env perl
package Bio::MLST::Bin::Download;
$Bio::MLST::Bin::Download::VERSION = '2.1.1706216';
# ABSTRACT: Downloads all the MLST databases to disk. It requires access to the Internet.
# PODNAME: download_mlst_databases
BEGIN { unshift( @INC, '../lib' ) }
use lib "/software/pathogen/internal/prod/lib";
use Moose;
use Getopt::Long;
use Bio::MLST::DatabaseSettings;
use Bio::MLST::Download::Databases;
my ($config_file, $base_directory, $help, $version);
GetOptions ('c|config=s'         => \$config_file,
            'b|base_directory=s' => \$base_directory,
            'h|help'             => \$help,
            'v|version'          => \$version,
);
(! $version ) or die "$0 version " . Bio::MLST::Bin::Download->VERSION . "\n";
(! $help)or die <<USAGE;
Usage: download_mlst_databases [options]
   -c STR Config file containing details of MLST databases from pubMLST
   -b STR Directory where MLST databases are stored [\$MLST_DATABASES]
   -h     Print this message and exit
   -v     Print version number and exit
USAGE
;
$base_directory ||= $ENV{MLST_DATABASES};
$base_directory ||= '/lustre/scratch108/pathogen/pathpipe/mlst';
$config_file    ||= 'https://pubmlst.org/data/dbases.xml';
my $database_settings = Bio::MLST::DatabaseSettings->new(filename => $config_file)->settings;
my $databases = Bio::MLST::Download::Databases->new(
  databases_attributes => $database_settings,
  base_directory  => $base_directory
);
$databases->update();
__END__
=pod
=encoding UTF-8
=head1 NAME
download_mlst_databases - Downloads all the MLST databases to disk. It requires access to the Internet.
=head1 VERSION
version 2.1.1706216
=head1 SYNOPSIS
Downloads all the MLST databases to disk. It requires access to the Internet.
    # download everything with defaults
    download_mlst_databases
    # print version
    download_mlst_databases -v
    # XML file containing details of the MLST databases (from pubmlst)
    download_mlst_databases -c my_config_file.json
    # destination base directory defaults to the environment variable \$MLST_DATABASES
    download_mlst_databases -b /path/to/destination
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
  The GNU General Public License, Version 3, June 2007
=cut