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revision 1.2, Fri Oct 5 17:25:53 2007 UTC revision 1.4, Fri Oct 12 20:23:04 2007 UTC
# Line 36  Line 36 
36  my $crit_bin = "/vol/critica/bin";  my $crit_bin = "/vol/critica/bin";
37  my $crit_scripts = "/vol/critica/scripts";  my $crit_scripts = "/vol/critica/scripts";
38    
39    #
40    # need to set up the PERL5LIB for our children so critica can find stuff
41    # installed in the perl environment.
42    #
43    
44    $ENV{PERL5LIB} = join(":", @INC);
45    $ENV{PATH} = join(":", $ENV{PATH}, $FIG_Config::bin, $FIG_Config::ext_bin);
46    
47  $ENV{CRITICA_BLASTN} = "$FIG_Config::ext_bin/blastall -p blastn";  $ENV{CRITICA_BLASTN} = "$FIG_Config::ext_bin/blastall -p blastn";
48  $ENV{CRITICA_BLASTPARM} = "-gF -e1e-4";  $ENV{CRITICA_BLASTPARM} = "-gF -e1e-4";
49  $ENV{CRITICA_BLASTDB} = "-d $nt -i";  $ENV{CRITICA_BLASTDB} = "-d $nt -i";
# Line 105  Line 113 
113    
114  $meta->add_log_entry($0, "finish critica computation on $jobdir");  $meta->add_log_entry($0, "finish critica computation on $jobdir");
115  $meta->set_metadata("status.critica", "complete");  $meta->set_metadata("status.critica", "complete");
116    $meta->set_metadata("critica.running", "no");
117  exit(0);  exit(0);
118    
119    
# Line 124  Line 133 
133      {      {
134          $meta->add_log_entry($0, ['fatal error', $msg]);          $meta->add_log_entry($0, ['fatal error', $msg]);
135          $meta->set_metadata("status.critica", "error");          $meta->set_metadata("status.critica", "error");
136            $meta->set_metadata("critica.running", "no");
137      }      }
138    
139      croak "$0: $msg";      croak "$0: $msg";

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