[Bio] / FigKernelScripts / svr_run_RAST_jobs.pl Repository:
ViewVC logotype

Diff of /FigKernelScripts/svr_run_RAST_jobs.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.3, Tue Dec 8 02:11:31 2009 UTC revision 1.5, Mon Jan 18 23:32:09 2010 UTC
# Line 7  Line 7 
7  use RASTserver;  use RASTserver;
8  use strict;  use strict;
9  use Data::Dumper;  use Data::Dumper;
10    use Getopt::Long;
11    
12    my $usage = "Usage: $0 [--url server-url] [--nonActive] [--verbose] [--test] username password < contig-id-list\n";
13    
14    my $verbose;
15  my $use_test_server = 0;  my $use_test_server = 0;
16  if (@ARGV && ($ARGV[0] =~ m/-test/o)) {  my $non_active = 0;
17      shift @ARGV;  my $url;
18      $use_test_server = 1;  if (!GetOptions('verbose'   => \$verbose,
19                    "nonActive" => \$non_active,
20                    "url=s" => \$url,
21                    'test'      => \$use_test_server))
22    {
23        die $usage;
24  }  }
25    
26  @ARGV == 2 or die "Usage: $0 [-test] username password < contig-id-list\n";  @ARGV == 2 or die $usage;
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 118  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";

Legend:
Removed from v.1.3  
changed lines
  Added in v.1.5

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3