[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 1.11, Mon May 18 16:54:56 2009 UTC revision 1.14, Mon Jan 4 20:30:23 2010 UTC
# Line 58  Line 58 
58  #  #
59    
60  my $keep_genecalls = $meta->get_metadata("keep_genecalls");  my $keep_genecalls = $meta->get_metadata("keep_genecalls");
61    my $call_using_glimmer = $meta->get_metadata("use_glimmer");
62  my $unformatted = "$raw_dir/unformatted_contigs";  my $unformatted = "$raw_dir/unformatted_contigs";
63    
64  if (! -f $unformatted)  if (! -f $unformatted)
# Line 119  Line 120 
120  #  #
121    
122  my $tmp = "tmprp.job$job.$$";  my $tmp = "tmprp.job$job.$$";
123  my $tmpdir = "/scratch/$tmp";  #my $tmpdir = "/scratch/$tmp";
124    my $tmpdir = "$FIG_Config::temp/$tmp";
125    
126  &FIG::verify_dir("$jobdir/rp");  &FIG::verify_dir("$jobdir/rp");
127    
# Line 154  Line 156 
156      }      }
157  }  }
158    
159    
160    #
161    # If we are to call using glimmer instead of the usual mechanism, first
162    # invoke call_genome_using_glimmer.
163    #
164    
165    if ($call_using_glimmer)
166    {
167        my @cmd = ("$FIG_Config::bin/call_genome_using_glimmer",
168                   "--glimmerV=3",
169                   "--code=$genetic_code",
170                   "--meta=$meta_file",
171                   $raw_dir);
172    
173        print "Run @cmd\n";
174        $meta->add_log_entry($0, ['running', @cmd]);
175    
176        $rc = system(@cmd);
177    
178        if ($rc != 0)
179        {
180            &fatal("call_using_glimmer command failed with rc=$rc: @cmd\n");
181        }
182    }
183    
184  for my $key (grep { /^status\.rp\./ } $meta->get_metadata_keys())  for my $key (grep { /^status\.rp\./ } $meta->get_metadata_keys())
185  {  {
186      my $old = $meta->get_metadata($key);      my $old = $meta->get_metadata($key);

Legend:
Removed from v.1.11  
changed lines
  Added in v.1.14

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3