Changeset 275

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Timestamp:
10/12/09 14:06:24 (1 month ago)
Author:
cholt
Message:

added some changes to how tmp is used and fixed blastrm params

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  • lib/GI.pm

    r274 r275  
    5454sub set_global_temp { 
    5555    my $dir = shift; 
     56 
     57    return if(! -d $dir); 
     58 
     59    #remove old tempdir if user supplied a new one 
     60    if($TMP ne $dir){ 
     61        File::Path::rmtree($TMP); 
     62    } 
    5663 
    5764    $TMP = $dir; 
    …… 
    28432850   } 
    28442851    
    2845    #--set up optional global TMP 
     2852   #--set up optional global TMP (If TMP is not accessible from other nodes 
     2853   #) 
    28462854   if($CTL_OPT{TMP}){ 
    28472855       $CTL_OPT{_TMP} = tempdir("maker_XXXXXX", CLEANUP => 1, DIR => $CTL_OPT{TMP}); 
    2848        set_global_temp($CTL_OPT{_TMP}); 
    2849    } 
     2856   } 
     2857   else{ 
     2858       $CTL_OPT{_TMP} = $TMP; 
     2859   } 
     2860 
     2861   set_global_temp($CTL_OPT{_TMP}); 
    28502862 
    28512863   #---set up blast databases and indexes for analyisis 

  • lib/Widget/RepeatMasker.pm

    r273 r275  
    99use FileHandle; 
    1010use Widget; 
    11 #use Bio::DB::Fasta; 
    1211use Bio::Search::Hit::PhatHit::repeatmasker; 
    1312use Bio::Search::HSP::PhatHSP::repeatmasker; 
    …… 
    251250        #checks if RepeatMasker really finished 
    252251        unless($count){ 
    253             unlink($file); 
    254             die "ERROR: The file $file appears to be incomplete\n". 
    255                 "MAKER will need to delete the file, before trying again\n\n"; 
     252            #unlink($file); 
     253            #die "ERROR: The file $file appears to be incomplete\n". 
     254            #    "MAKER will need to delete the file, before trying again\n\n"; 
    256255        } 
    257256 

  • lib/runlog.pm

    r272 r275  
    264264 
    265265                #temp lamprey 
    266                 $log_val =~ s/^\/*scratch\/serial[^\/]*\/u0045039\/lamprey2\/*//; 
    267                 $ctl_val =~ s/^\/*scratch\/serial[^\/]*\/u0045039\/lamprey2\/*//; 
     266                $log_val =~ s/^\/*scratch\/serial[^\/]*\/u0045039\///; 
     267                $ctl_val =~ s/^\/*scratch\/serial[^\/]*\/u0045039\///; 
    268268                 
    269269                #if previous log options are not the same as current control file options 
    …… 
    378378                        "did not finish on the last run and must be erased\n"; 
    379379                    #temp lamprey 
    380                     $key =~ s/^\/*scratch\/serial[^\/]*\/u0045039\/lamprey2\/*//; 
     380                    $key =~ s/^\/*scratch\/serial[^\/]*\/.*\/([^\/]*.maker.output)/$1/; 
    381381 
    382382                    push(@files, $key);