===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-258-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm:259:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-260-    #AMAP version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-339-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm:340:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Amap.pm-341-    my $outfile = $self->outfile_name(); 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Blat.pm-572-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Blat.pm:573:    my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Blat.pm-574-    $self->throw( "Blat call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-197-    return undef unless defined $exe;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm:198:    my $string = `$exe -- ` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-199-    $string =~ /\(([\d.]+)\)/;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-277-    $self->debug( "dba command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm:278:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/DBA.pm-279-    $self->throw( "DBA call ($commandstring) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-187-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm:188:    my $string = `$exe -v` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-189-    #exonerate from exonerate version 2.0.0\n...
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-247-     $self->debug( "$str\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm:248:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Exonerate.pm-249-     $self->throw( "Exonerate call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-486-            -e $orig || $self->throw("Strange, $orig doesn't seem to exist");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:487:            system("cp $orig $orig.bk") && $self->throw("Backup of $orig failed: $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:488:            system("cp $matrix_file $orig") && $self->throw("Copy of $matrix_file -> $orig failed: $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-489-        }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-510-    $self->debug("$command_string\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:511:    my $status = system(($version <= 3 ? '_POSIX2_VERSION=1 ' : '').$command_string); # temporary hack whilst lagan script 'rechaos.pl' uses obsolete sort syntax
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-512-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-514-        my $orig = File::Spec->catfile($PROGRAM_DIR, 'nucmatrix.txt');
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm:515:        system("mv $orig.bk $orig") && $self->warn("Restore of $orig from $orig.bk failed: $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Lagan.pm-516-    }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MAFFT.pm-383-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MAFFT.pm:384:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MAFFT.pm-385-    my $outfile = $self->outfile();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-210-    return unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm:211:    my $string = `$exe -version 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-212-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-526-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm:527:    my $status  = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/MSAProbs.pm-528-    my $outfile = $self->outfile_name; 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-226-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm:227:    my $string = `$exe 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-228-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-429-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm:430:    my $status  = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Muscle.pm-431-    my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm-267-    
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm:268:    system($command) && $self->throw("pal2nal call ($command) failed: $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm-269-    open(my $errfh, '<', $error_file);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-247-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm:248:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-249-    #PROBALIGN version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-328-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm:329:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probalign.pm-330-    my $outfile = $self->outfile_name(); 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-276-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm:277:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-278-    #PROBCONS version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-357-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm:358:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Probcons.pm-359-    if ($status) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-247-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm:248:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-249-    #PRODA version 1.09 - align multiple protein sequences and print to standard output
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-328-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm:329:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Proda.pm-330-    my $outfile = $self->outfile_name(); 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Sim4.pm-295-    $self->debug( "Sim4 command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Sim4.pm:296:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Sim4.pm-297-    $self->throw( "Sim4 call ($commandstring) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-322-		}
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm:323:		my $status = system($para);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-324-		$self->throw("$para crashed:  $?\n" )unless ($status==0);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-359-		}
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm:360:		my $status = system($para);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm-361-		$self->throw("$para crashed:  $?\n" )unless ($status==0);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-258-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm:259:    my $string = `$exe --show 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-260-    $string =~ /Kalign\s+\((\d+)\..+\)/m;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-345-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm:346:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Alignment/Kalign.pm-347-    my $outfile = $self->outfile_name(); 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Coil.pm-271-     }
bioperl-run-1.7.3/lib/Bio/Tools/Run/Coil.pm:272:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Coil.pm-273-     $self->throw( "Coil call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSApplication.pm-230-	$self->debug( "Command line: ", $runstring, "\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSApplication.pm:231:	return `$runstring`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSApplication.pm-232-}
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-171-	# reading from EMBOSS program acdc stdout (prior to version 2.8.0)
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm:172:	$file = `acdc $prog -help -verbose -acdtable 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-173-    } else {
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-174-	# reading from EMBOSS program acdtable stdout (version 2.8.0 or greater)
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm:175:	$file = `acdtable $prog -help -verbose 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/EMBOSSacd.pm-176-    }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/ERPIN.pm-304-        local $SIG{CHLD} = 'DEFAULT';
bioperl-run-1.7.3/lib/Bio/Tools/Run/ERPIN.pm:305:        my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/ERPIN.pm-306-        if($status || !-e $outfile || -z $outfile ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Eponine.pm-399-		 " \n Check your java version, it has to be version 1.2 or later. Eponine crashed ($cmd) crashed: $? \n")
bioperl-run-1.7.3/lib/Bio/Tools/Run/Eponine.pm:400:	if (system ($cmd));
bioperl-run-1.7.3/lib/Bio/Tools/Run/Eponine.pm-401-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/FootPrinter.pm-352-  
bioperl-run-1.7.3/lib/Bio/Tools/Run/FootPrinter.pm:353:  my $status = system($cmd_str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/FootPrinter.pm-354-  $self->throw("FootPrinter Call($cmd_str) crashed: $?\n") 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-210-    my $prog = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm:211:    my $string = `$prog -version`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-212-    if( $string =~ /Version:\s+\$\s*Name:\s+(\S+)\s+\$/ ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-303-    $self->debug("genewise command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm:304:    my $status = system("$commandstring > $outfile1");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Genewise.pm-305-    $self->throw("Genewise call $commandstring crashed: $? \n") unless $status == 0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-425-            if ($progname eq 'hmmbuild') {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm:426:                my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-427-                return $status ? 0 : 1;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-429-            else {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm:430:                system($str) && $self->throw("HMMER call ($str) crashed: $?\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-431-                @in = (-file => $outfile);
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-459-        $str .= " > $null 2> $null" if $self->quiet;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm:460:        my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Hmmer.pm-461-        return $status ? 0 : 1;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-489-    my $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:490:    my $string = `$exe -h 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-491-    my $v;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-988-    if ($out) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:989:        my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-990-        if($status || !-e $out || -z $out ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-1077-    for my $exec (qw(cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat)) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:1078:        my $output = `$exec --devhelp`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-1079-        if ($?) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm:1080:            $output = `$exec -h`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Infernal.pm-1081-        }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-268-    my $cmd = "align2binomial.pl $offset $gtf $aln_file > $binomial_file 2> $error_file";
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:269:    #system("rm -fr $cwd/mcs_dir; cp -R $temp_dir $cwd/mcs_dir");
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:270:    my $throw = system($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-271-    open(my $efh, "<", $error_file) || $self->throw("Could not open error file '$error_file'");
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-282-    my $phylo_file = 'align_name.phylo';
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:283:    system("generate_phyloMAX_score.pl $binomial_file > $phylo_file") && $self->throw("generate_phyloMAX_score.pl call failed: $?, $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-284-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-288-    my $bed_file = 'align_name.bed'; # hardcoded in generate_mcs_beta.pl
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm:289:    system("generate_mcs_beta.pl $offset $gtf $phylo_file > $mcs_file") && $self->throw("generate_mcs_beta.pl failed: $?, $!");
bioperl-run-1.7.3/lib/Bio/Tools/Run/MCS.pm-290-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-234-        $mxprf_file = 'mxprf';
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm:235:        system("$exe $mxlib ignored ignored $mxprf_file -p @thresh") && $self->throw("Something went wrong whist creating profile: $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-236-    }
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-248-    
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm:249:    system($cmd_line) && $self->throw("Something went wrong whist running '$cmd_line': $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Match.pm-250-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-181-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm:182:    my $string = `$exe 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-183-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-233-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm:234:    my $status  = system($command);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/FastTree.pm-235-    my $outfile = $self->outfile_name();
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-255-        #    alarm 60;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm:256:        #    system($command) && $self->throw("gerp call ($command) failed: $! | $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-257-        #    alarm 0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-263-        #
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm:264:        # system("rm -fr $cwd/gerp_dir; cp -R $temp_dir $cwd/gerp_dir");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-265-        
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-285-    
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm:286:    #system("rm -fr $cwd/gerp_dir; cp -R $temp_dir $cwd/gerp_dir");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Gerp.pm-287-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm-371-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm:372:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Njtree/Best.pm-373-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-387-    $self->debug("phastCons training command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm:388:    system($command) && $self->throw("phastCons training call ($command) crashed: $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-389-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-392-    $self->debug("phastCons command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm:393:    system($command) && $self->throw("phastCons call ($command) crashed: $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm-394-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm-296-    $self->debug("phyloFit command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm:297:    system($command) && $self->throw("phyloFit call ($command) crashed: $?");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm-298-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-335-    my $exe = $self->executable || return;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm:336:    my $string = substr `$exe -h`, 0, 40;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-337-    my ($version) = $string =~ /PhyML v([\d+\.]+)/;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-969-    $self->debug("Phyml command = $command\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm:970:    `$command`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Phyml.pm-971-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-189-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm:190:    my $string = `$exe -v 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-191-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-256-
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm:257:    my $status  = system($command);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Phylo/Raxml.pm-258-	
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-192-    return undef unless defined $exe;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm:193:    my $string = `$exe -v ` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-194-    $string =~ /\(([\d.]+)\)/;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-264-    $self->debug( "primate command = $commandstring");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm:265:    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primate.pm-266-    $self->throw( "primate call ($commandstring) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primer3.pm-556-    if (!defined $self->{'_progversion'}) {
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primer3.pm:557:        my $string = `$exe -about 2>&1`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Primer3.pm-558-        my $v;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Prints.pm-247-     my $str =$self->executable." ".$self->DB." ".$self->_input." -fjR >".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Prints.pm:248:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Prints.pm-249-     $self->throw( "Prints call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Profile.pm-245-     my $str =$self->executable.' -fz '.$self->_input." ".$self->DB." > ".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Profile.pm:246:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Profile.pm-247-     $self->throw( "Profile call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Promoterwise.pm-197-    my $prog = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Promoterwise.pm:198:    my $string = `$prog -version`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Promoterwise.pm-199-    $string =~ /(Version *)/i;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm-270-    $self->debug( "pseudowise command = $commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm:271:#    my $status = system($commandstring);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm:272:    `$commandstring`;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Pseudowise.pm-273-#    $self->throw( "Pseudowise call ($commandstring) crashed: $? \n") 
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/RNAMotif.pm-394-        local $SIG{CHLD} = 'DEFAULT';
bioperl-run-1.7.3/lib/Bio/Tools/Run/RNAMotif.pm:395:        my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/RNAMotif.pm-396-        if($status || !-e $outfile ) {
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-230-    return undef unless $exe;
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm:231:    my $string = `$exe -- ` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-232-    if( $string =~ /\(([\d.]+)\)/ ||
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-304-  }
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm:305:  my $status = system($cmd_str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/RepeatMasker.pm-306-  $self->throw("Repeat Masker Call($cmd_str) crashed: $?\n")
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Seg.pm-236-     my $str =$self->executable." ".$self->_input." -l > ".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Seg.pm:237:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Seg.pm-238-     $self->throw( "Seg call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Signalp.pm-250-     my $str =$self->executable." -t euk -trunc 50 ".$self->{'input'}." > ".$outfile;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Signalp.pm:251:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Signalp.pm-252-     $self->throw( "Signalp call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Simprot.pm-440-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Simprot.pm:441:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/lib/Bio/Tools/Run/Simprot.pm-442-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm-440-	$self->debug("$commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm:441:	system($commandstring) && $self->throw("$executable call crashed: $? | $! | $commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm-442-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneWUBlast.pm-249-	$self->debug("$commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneWUBlast.pm:250:	system($commandstring) && $self->throw("$executable call crashed: $? | $! | $commandstring\n");
bioperl-run-1.7.3/lib/Bio/Tools/Run/StandAloneWUBlast.pm-251-    
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Tmhmm.pm-294-     
bioperl-run-1.7.3/lib/Bio/Tools/Run/Tmhmm.pm:295:     my $status = system($str);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Tmhmm.pm-296-     $self->throw( "Tmhmm call ($str) crashed: $? \n") unless $status==0;
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-667-
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm:668:  my $status = system($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-669-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-709-  $cmd .= " > $null";
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm:710:  my $status = system($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/TribeMCL.pm-711-
##############################################
bioperl-run-1.7.3/lib/Bio/Tools/Run/Vista.pm-547-    $self->debug($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Vista.pm:548:	 my $status = system ($cmd);
bioperl-run-1.7.3/lib/Bio/Tools/Run/Vista.pm-549-
##############################################
bioperl-run-1.7.3/scripts/bp_blast2tree.pl-44-GetOptions(
bioperl-run-1.7.3/scripts/bp_blast2tree.pl:45:	   'h|help'       => sub { exec('perldoc', $0);
bioperl-run-1.7.3/scripts/bp_blast2tree.pl-46-				   exit(0); },
##############################################
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-66-# Print documentation if help switch was given
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS:67:exec('perldoc', $0) and exit() if $opt_h;
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-68-
##############################################
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-112-    print "--> Performing hmmsearch in file:\t\t$line\n";
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS:113:    system("$hmmsearch $opt_p $line > multi/$out.hmms");
bioperl-run-1.7.3/scripts/multi_hmmsearch.PLS-114-    print "==> hmmsearch results stored in file:\t\tmulti/$out.hmms\n";
##############################################
bioperl-run-1.7.3/scripts/run_neighbor.PLS-38-	   'o|out:s'   => \$out,
bioperl-run-1.7.3/scripts/run_neighbor.PLS:39:	   'h|help'    => sub { exec('perldoc',$0); exit(0) }
bioperl-run-1.7.3/scripts/run_neighbor.PLS-40-	   );
##############################################
bioperl-run-1.7.3/scripts/run_protdist.PLS-47-	   'i|in:s'    =>  \$file,
bioperl-run-1.7.3/scripts/run_protdist.PLS:48:	   'h|help'    => sub { exec('perldoc',$0); exit(0) }
bioperl-run-1.7.3/scripts/run_protdist.PLS-49-	   );
##############################################
bioperl-run-1.7.3/t/DrawGram.t-27-	if( test_debug() ) {
bioperl-run-1.7.3/t/DrawGram.t:28:		`gs $file`;
bioperl-run-1.7.3/t/DrawGram.t-29-	}
##############################################
bioperl-run-1.7.3/t/DrawGram.t-44-	if( test_debug() ) {
bioperl-run-1.7.3/t/DrawGram.t:45:		`gs $file`;
bioperl-run-1.7.3/t/DrawGram.t-46-	}
##############################################
bioperl-run-1.7.3/t/DrawTree.t-26-	if( test_debug() ) {
bioperl-run-1.7.3/t/DrawTree.t:27:		`gs $file`;
bioperl-run-1.7.3/t/DrawTree.t-28-	} else { 
##############################################
bioperl-run-1.7.3/t/DrawTree.t-38-	if( test_debug() ) {
bioperl-run-1.7.3/t/DrawTree.t:39:		`gs $file`;
bioperl-run-1.7.3/t/DrawTree.t-40-	} else { 
##############################################
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch-15-     return undef unless $exe = $self->executable;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch:16:-    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch-17--    $string =~ /Kalign\s+version\s+(\d+\.\d+)/m;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch:18:+    my $string = `$exe --show 2>&1` ;
bioperl-run-1.7.3/debian/patches/kalign-version-regex.patch-19-+    $string =~ /Kalign\s+\((\d+)\..+\)/m;
##############################################
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-258-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:259:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-260-    $string =~ /Kalign\s+version\s+(\d+\.\d+)/m;
##############################################
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-345-
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:346:    my $status = system($commandstring);
bioperl-run-1.7.3/.pc/kalign-input-via-piping.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-347-    my $outfile = $self->outfile_name(); 
##############################################
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-258-    return undef unless $exe = $self->executable;
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:259:    my $string = `$exe 2>&1` ;
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-260-    $string =~ /Kalign\s+version\s+(\d+\.\d+)/m;
##############################################
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-345-
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm:346:    my $status = system($commandstring);
bioperl-run-1.7.3/.pc/kalign-version-regex.patch/lib/Bio/Tools/Run/Alignment/Kalign.pm-347-    my $outfile = $self->outfile_name();