[Bio] / FortyEight / rp_rapid_propagation.pl Repository:
ViewVC logotype

Diff of /FortyEight/rp_rapid_propagation.pl

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

revision 1.19, Wed Sep 29 16:21:04 2010 UTC revision 1.21, Wed Sep 28 20:45:32 2011 UTC
# Line 191  Line 191 
191  my $user = &FIG::file_head("$jobdir/USER");  my $user = &FIG::file_head("$jobdir/USER");
192  chomp $user;  chomp $user;
193    
194    #
195    # Determine if we are choosing a kmer dataset.
196    #
197    
198    my $kmerDataset;
199    my @opt_kmer_dataset;
200    if (my $ds = $meta->get_metadata('options.figfam_version'))
201    {
202        $kmerDataset = $ds;
203        $ENV{SVR_DEFAULT_KMER_DATASET} = $ds;
204        @opt_kmer_dataset = (-kmerDataset => $ds);
205    }
206    
207  my $rp_script = $FIG_Config::rapid_propagation_script{$user};  my $rp_script = $FIG_Config::rapid_propagation_script{$user};
208  $rp_script = $FIG_Config::rapid_propagation_script if $rp_script eq '';  $rp_script = $FIG_Config::rapid_propagation_script if $rp_script eq '';
209  my %valid_rapid_propagation = (rapid_propagation => 1,  my %valid_rapid_propagation = (rapid_propagation => 1,
210                                 rapid_propagation2 => 1,                                 rapid_propagation2 => 1,
211                                 rapid_propagation3 => 1,                                 rapid_propagation3 => 1,
212                                 rapid_propagation4 => 1,                                 rapid_propagation4 => 1,
213                                   rapid_propagation5 => 1,
214                                );                                );
215    
216  if (!$valid_rapid_propagation{$rp_script})  if (!$valid_rapid_propagation{$rp_script})
217  {  {
218      $rp_script = "rapid_propagation";      &fatal("invalid rapid_propagation script $rp_script\n");
219  }  }
220    
221  $meta->add_log_entry($0, "Processing using rapid propagation script '$rp_script'");  $meta->add_log_entry($0, "Processing using rapid propagation script '$rp_script'");
222  @cmd = ("$FIG_Config::bin/$rp_script", "--errdir", $errdir,  @cmd = ("$FIG_Config::bin/$rp_script", "--errdir", $errdir,
223          @keep_genecalls_flag,          @keep_genecalls_flag,
224            @opt_kmer_dataset,
225          "--code", $genetic_code,          "--code", $genetic_code,
226          "--meta", $meta_file,          "--meta", $meta_file,
227          "--tmpdir", $tmpdir,          "--tmpdir", $tmpdir,

Legend:
Removed from v.1.19  
changed lines
  Added in v.1.21

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3