[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 1.2, Wed Feb 14 14:02:06 2007 UTC revision 1.4, Fri Jun 1 16:26:26 2007 UTC
# Line 15  Line 15 
15    
16  -d $jobdir or die "$0: job dir $jobdir does not exist\n";  -d $jobdir or die "$0: job dir $jobdir does not exist\n";
17    
18    my $hostname = `hostname`;
19    chomp $hostname;
20    
21  my $genome = &FIG::file_head("$jobdir/GENOME_ID");  my $genome = &FIG::file_head("$jobdir/GENOME_ID");
22  chomp $genome;  chomp $genome;
23  $genome =~ /^\d+\.\d+/ or die "$0: Cannnot find genome ID for jobdir $jobdir\n";  $genome =~ /^\d+\.\d+/ or die "$0: Cannnot find genome ID for jobdir $jobdir\n";
# Line 35  Line 38 
38      &fatal("raw genome directory $raw_dir does not exist");      &fatal("raw genome directory $raw_dir does not exist");
39  }  }
40    
41    $meta->set_metadata("rp.hostname", $hostname);
42    
43  #  #
44  # Perform the rapid propagation.  # Perform the rapid propagation.
# Line 84  Line 88 
88    
89  &FIG::verify_dir("$jobdir/rp");  &FIG::verify_dir("$jobdir/rp");
90    
91    #
92    # Determine if we are keeping the original gene calls.
93    #
94    
95    my $keep_genecalls = $meta->get_metadata("keep_genecalls");
96    my @keep_genecalls_flag;
97    
98    if ($keep_genecalls)
99    {
100        $meta->add_log_entry($0, "Keeping original gene calls");
101        @keep_genecalls_flag = ("--keep");
102    }
103    
104  @cmd = ("$FIG_Config::bin/rapid_propagation", "--errdir", $errdir,  @cmd = ("$FIG_Config::bin/rapid_propagation", "--errdir", $errdir,
105          "--meta", $meta_file, "--tmpdir", $tmpdir, $raw_dir, $rp_dir);          @keep_genecalls_flag,
106            "--meta", $meta_file,
107            "--tmpdir", $tmpdir,
108            $raw_dir, $rp_dir);
109  print "Run @cmd\n";  print "Run @cmd\n";
110  $meta->add_log_entry($0, ['running', @cmd]);  $meta->add_log_entry($0, ['running', @cmd]);
111    

Legend:
Removed from v.1.2  
changed lines
  Added in v.1.4

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3