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revision 1.4, Thu Dec 10 19:31:12 2009 UTC revision 1.5, Mon Jan 18 23:32:09 2010 UTC
# Line 9  Line 9 
9  use Data::Dumper;  use Data::Dumper;
10  use Getopt::Long;  use Getopt::Long;
11    
12  my $usage = "Usage: $0 [--verbose] [--test] username password < contig-id-list\n";  my $usage = "Usage: $0 [--url server-url] [--nonActive] [--verbose] [--test] username password < contig-id-list\n";
13    
14  my $verbose;  my $verbose;
15  my $use_test_server = 0;  my $use_test_server = 0;
16    my $non_active = 0;
17    my $url;
18  if (!GetOptions('verbose' => \$verbose,  if (!GetOptions('verbose' => \$verbose,
19                    "nonActive" => \$non_active,
20                    "url=s" => \$url,
21                  'test' => \$use_test_server))                  'test' => \$use_test_server))
22  {  {
23      die $usage;      die $usage;
# Line 23  Line 27 
27    
28  my $username = shift;  my $username = shift;
29  my $password = shift;  my $password = shift;
30    my $opts = {};
31  my $rast = RASTserver->new($username, $password, { -test => $use_test_server});  if ($url)
32    {
33        $opts->{-server} = $url;
34    }
35    if ($use_test_server)
36    {
37        $opts->{-test} = 1;
38    }
39    my $rast = RASTserver->new($username, $password, $opts);
40    
41  my @input_ids = <STDIN>;  my @input_ids = <STDIN>;
42  chomp @input_ids;  chomp @input_ids;
# Line 123  Line 135 
135          -geneticCode => $biggest->{genetic_code},          -geneticCode => $biggest->{genetic_code},
136          -keepGeneCalls => 0,          -keepGeneCalls => 0,
137          -geneCaller => 'RAST',          -geneCaller => 'RAST',
138            -nonActive => $non_active,
139      };      };
140    
141      print "Submitting job to RAST for contigs @$ids with these parameters:\n";      print "Submitting job to RAST for contigs @$ids with these parameters:\n";

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