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revision 1.25, Mon Nov 17 18:31:54 2008 UTC revision 1.26, Thu Nov 20 16:28:42 2008 UTC
# Line 2874  Line 2874 
2874    
2875      unless ($dont_copy)      unless ($dont_copy)
2876      {      {
2877          # create soft links for each genome-specific path, with the same name          # copy each genome-specific path, with the same name as the path in the "All" directory
         # as the path in the "All" directory  
2878          foreach my $path (@genome_paths)          foreach my $path (@genome_paths)
2879          {          {
2880              my $temp_sdg = $scenario_dir_genome;              my $temp_sdg = $scenario_dir_genome;
# Line 2884  Line 2883 
2883              my $temp_sda = $scenario_dir_all;              my $temp_sda = $scenario_dir_all;
2884              $temp_sda =~ s/\(/\\\(/g;              $temp_sda =~ s/\(/\\\(/g;
2885              $temp_sda =~ s/\)/\\\)/g;              $temp_sda =~ s/\)/\\\)/g;
2886              `ln -s $temp_sda/$path $temp_sdg`;              `cp -r $temp_sda/$path $temp_sdg`;
2887          }          }
2888      }      }
2889    
# Line 3714  Line 3713 
3713      my ($genome_id) = @_;      my ($genome_id) = @_;
3714      my $scenario_dir = get_scenario_directory($genome_id);      my $scenario_dir = get_scenario_directory($genome_id);
3715      my $pathinfo_dir = $scenario_dir  . "/PathInfo";      my $pathinfo_dir = $scenario_dir  . "/PathInfo";
3716        my @paths = `find $pathinfo_dir -type d -name "path_*"`;
     #  
     # Mac and Linux don't have the same find options for following symlinks.  
     #  
     my $uname = `uname`;  
     my @paths;  
     if ($uname =~ /^Darwin/)  
     {  
         @paths = `find -L $pathinfo_dir -type d -name "path_*"`;  
     }  
     else  
     {  
         @paths = `find $pathinfo_dir -follow -type d -name "path_*"`;  
     }  
   
3717      my %inputs;      my %inputs;
3718      my %outputs;      my %outputs;
3719    

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