diff --git a/install.pl b/install.pl
index 255883a..e42d6f4 100755
--- a/install.pl
+++ b/install.pl
@@ -1,17 +1,15 @@
 #!/usr/bin/env perl
 
-
-
 use strict;
 use warnings;
-use LWP::Simple;
 
 print STDERR "\n
 ###############################################################################################
-# Last update: May 18, 2016
-# This is the miRDeep2 installer. 
+# Last update: Apr 10, 2017
+# This is the miRDeep2 installer
 # It is tested under a bash and zsh shell
-# It will try to download all necessary files and install them. 
+# It will try to download all necessary third-party tools and install them. 
+# To run this installer you need to have mirdeep2.0.0.8 or later
 #
 ###############################################################################################
 
@@ -23,7 +21,6 @@
 my $new='no';
 
 $new = $ARGV[0] if($ARGV[0]);
-
 my $shell=$ENV{'SHELL'};
 my $shellconf='.bash_profile';
 if($shell =~ /zsh/){
@@ -35,43 +32,43 @@
 		die "Could not determine file for setting environment variables\n";
 	}
 }
-			
+
 
 
 if($new !~ /no/){
-    print STDERR "making backup of .bashrc,$shellconf and .cshrc and removing all entries of mirdeep in those files\n";
-    rem_mirdeep(".bashrc");
-    rem_mirdeep("$shellconf");
-    rem_mirdeep(".cshrc");
+	print STDERR "making backup of .bashrc,$shellconf and .cshrc and removing all entries of mirdeep in those files\n";
+	rem_mirdeep(".bashrc");
+	rem_mirdeep("$shellconf");
+	rem_mirdeep(".cshrc");
 }
 
 my $grep;
 $grep=`which grep`;
 if(not $grep){
-    $grep=`which ggrep`;
+	$grep=`which ggrep`;
 }
 if(not $grep){
-    die "No grep found on system\n";
+	die "No grep found on system\n";
 }
 chomp $grep;
 
 
 my $gcc=`gcc --version 2>&1`;
 if($gcc !~ /(GCC)/i and $gcc !~ /clang/i){
-    print STDERR "\nError:\n\tno gcc compiler installed. Please install a gcc compiler\n";
-    my $r=`uname -s`;
-    chomp $r;
-    if($r !~ /Linux/i){
-	print STDERR "==>     If you are using MacOS then you probably need to install Xcode with commandline-tools from the appstore!\n\n";
-    }
-    exit;
+	print STDERR "\nError:\n\tno gcc compiler installed. Please install a gcc compiler\n";
+	my $r=`uname -s`;
+	chomp $r;
+	if($r !~ /Linux/i){
+		print STDERR "==>     If you are using MacOS then you probably need to install Xcode with commandline-tools from the appstore!\n\n";
+	}
+	exit;
 }else{
-    if($gcc =~ /^gcc\s*\S*\s*(\d+\S+)\s*/){
-        print STDERR "gcc version: $1                                      already installed, nothing to do ...\n";
-    }
-    if($gcc =~ /clang/){
-	print STDERR "clang installed                                      already installed, nothing to do ...\n";
-    }
+	if($gcc =~ /^gcc\s*\S*\s*(\d+\S+)\s*/){
+		print STDERR "gcc version: $1                                      already installed, nothing to do ...\n";
+	}
+	if($gcc =~ /clang/){
+		print STDERR "clang installed                                      already installed, nothing to do ...\n";
+	}
 } 
 
 my %progs;
@@ -90,22 +87,22 @@
 
 if($wget =~ /URL/i){
 	$dtool ="wget";
-	
+
 }elsif($curl){
-	$dtool ="curl";
+	$dtool ="curl -L"; ## forces curl to follow redirections
 	$dopt=" -O";
 }else{
 	die "No commandline download tool found on your system. Please install wget or curl on your machine\n";
 }
 
 if(not -d 'bin'){
-    #creating bin directory which will also contain other executables in the end\n";
-    my $ret=system("cp -r src bin");
-    if(not $ret){ 
-	print STDERR "bin directory created successful\n";
-    }else{
-	die "Could not create binary directory\n";
-    }
+	#creating bin directory which will also contain other executables in the end\n";
+	my $ret=system("cp -r src bin");
+	if(not $ret){ 
+		print STDERR "bin directory created successful\n";
+	}else{
+		die "Could not create binary directory\n";
+	}
 }
 
 
@@ -120,36 +117,36 @@
 ## set install dir
 my $install_bin_dir="$dir/bin";
 foreach my $e(@ARGV){
-    if($e =~ /install-dir=(.+)/){
-	$install_bin_dir=$1;
-    }
+	if($e =~ /install-dir=(.+)/){
+		$install_bin_dir=$1;
+	}
 }
 
 if($install_bin_dir ne "$dir/bin"){
-    ## check if it is writable and existet
-    if(not -d $install_bin_dir){
-	print STDERR "The given installation directory by argument install-dir is not existent\nexecutable files will be put into $dir/bin instead\n";
-	$install_bin_dir="$dir/bin";
-    }else{	
-	chdir $install_bin_dir;
-	my $ret=system("touch mirdeep_test_file");
-	if(not $ret){
-	    system("rm mirdeep_test_file");
-	}else{
-	    print STDERR "The given installation directory by argument install-dir is either not existent or not writeable\nexectable files will be put into $dir/bin instead\n";
-	    $install_bin_dir="$dir/bin";
+	## check if it is writable and existent
+	if(not -d $install_bin_dir){
+		print STDERR "The given installation directory by argument install-dir is not existent\nexecutable files will be put into $dir/bin instead\n";
+		$install_bin_dir="$dir/bin";
+	}else{	
+		chdir $install_bin_dir;
+		my $ret=system("touch mirdeep_test_file");
+		if(not $ret){
+			system("rm mirdeep_test_file");
+		}else{
+			print STDERR "The given installation directory by argument install-dir is either not existent or not writeable\nexectable files will be put into $dir/bin instead\n";
+			$install_bin_dir="$dir/bin";
+		}
+		chdir "$dir";
 	}
-	chdir "$dir";
-    }
 }
 
 ## check if we have the install path in our files 
 $in=`$grep "$install_bin_dir" ~/$shellconf`;
 if(not $in){
-    my $ret=`$grep $install_bin_dir ~/$shellconf |$grep PATH`;
-    if(not $ret){
-	`echo 'export PATH=\$PATH:$install_bin_dir' >> ~/$shellconf`;
-    }
+	my $ret=`$grep $install_bin_dir ~/$shellconf |$grep PATH`;
+	if(not $ret){
+		`echo 'export PATH=\$PATH:$install_bin_dir' >> ~/$shellconf`;
+	}
 }
 
 ## add this temporarily to make perl installation possible on some systems
@@ -157,29 +154,29 @@
 my $g=`$grep PERL_MB_OPT ~/$shellconf \|$grep install_base `;
 if($g){
 }else{
-    print STDERR "adding variables PERL_MB_OPT,PERL_MM_OPT,PERL5LIB to $shellconf\n";
-    `echo >> ~/$shellconf`;
-    `echo 'PERL_MB_OPT=\"--install_base $ENV{'HOME'}/perl5\";export PERL_MB_OPT' >> ~/$shellconf`;
-    `echo 'PERL_MM_OPT=\"INSTALL_BASE=$ENV{'HOME'}/perl5\";export PERL_MM_OPT' >> ~/$shellconf`;
+	print STDERR "adding variables PERL_MB_OPT,PERL_MM_OPT,PERL5LIB to $shellconf\n";
+	`echo >> ~/$shellconf`;
+	`echo 'PERL_MB_OPT=\"--install_base $ENV{'HOME'}/perl5\";export PERL_MB_OPT' >> ~/$shellconf`;
+	`echo 'PERL_MM_OPT=\"INSTALL_BASE=$ENV{'HOME'}/perl5\";export PERL_MM_OPT' >> ~/$shellconf`;
 	$g=`grep $dir/lib/perl5 ~/$shellconf`;
 	if(not $g){
 		$g=`grep PERL5LIB ~/$shellconf`;
 		if(not $g){
-		 `echo 'export PERL5LIB=$dir/lib/perl5' >> ~/$shellconf`;
-		 }else{
-			 `echo 'export PERL5LIB=\$PERL5LIB:$dir/lib/perl5' >> ~/$shellconf`;
+			`echo 'export PERL5LIB=$dir/lib/perl5' >> ~/$shellconf`;
+		}else{
+			`echo 'export PERL5LIB=\$PERL5LIB:$dir/lib/perl5' >> ~/$shellconf`;
 		}	
-	 }
-	
+	}
+
 	`echo >> ~/$shellconf`;
-    print STDERR "please run the install.pl script again in a new terminal window or just type
-	
+	print STDERR "please run the install.pl script again in a new terminal window or just type
+
 	source ~/$shellconf
 	perl install.pl
 
 	so that the new environment variables are visible to the install.pl script\n";
 
-    exit;
+	exit;
 }
 
 $g=`$grep $dir/lib/perl5 ~/$shellconf`;
@@ -191,14 +188,14 @@
 		`echo 'export PERL5LIB=\$PERL5LIB:$dir/lib/perl5' >> ~/$shellconf`;
 	}	
 
-`echo >> ~/$shellconf`;
-print STDERR "please run the install.pl script again in a new terminal window or just type
+	`echo >> ~/$shellconf`;
+	print STDERR "please run the install.pl script again in a new terminal window or just type
 
-source ~/$shellconf
-perl install.pl
+	source ~/$shellconf
+	perl install.pl
 
-so that the new environment variables are visible to the install.pl script\n";
-exit;
+	so that the new environment variables are visible to the install.pl script\n";
+	exit;
 }
 
 my $in2;
@@ -212,7 +209,7 @@
 my $binnew=1;
 
 if(not -d "essentials"){
-    `mkdir essentials`;
+	`mkdir essentials`;
 }else{
 	$binnew=0;
 }
@@ -225,104 +222,101 @@
 
 my $bowtie_version="1.1.1";
 if($dtool =~ /curl/){
-    
 	`$dtool https://sourceforge.net/projects/bowtie-bio/files/bowtie/ > to_del`;
 }else{
-    `$dtool https://sourceforge.net/projects/bowtie-bio/files/bowtie/ -O to_del`;
+	`$dtool https://sourceforge.net/projects/bowtie-bio/files/bowtie/ -O to_del`;
 }
 open IN,"to_del" or die "No bowtie_file_info file found\n";
 while(<IN>){
-    if(/projects\/bowtie-bio\/files\/bowtie\/(\d\.\d+\.*\d*)\//){
-	$bowtie_version=$1;
-	last;
-    }
+	if(/projects\/bowtie-bio\/files\/bowtie\/(\d\.\d+\.*\d*)\//){
+		$bowtie_version=$1;
+		last;
+	}
 }
 close IN;
 
+$bowtie_version="1.1.1"; #we force this version, cause 1.2 needs the TBB lib installed 
+
+my $bv=$bowtie_version;
+if($bv =~ /(\d\.\d)\.0/){
+	$bv=$1;
+}
+
+
 my $ret=checkBIN("bowtie","Usage");
 if($ret == 0){
-    print STDERR "bowtie                                           already installed, nothing to do ...\n";
+	print STDERR "bowtie                                           already installed, nothing to do ...\n";
 	$progs{bowtie} = 1;
 }else{
-    if(not -d "bowtie-$bowtie_version"){
-
-        print STDERR "Downloading bowtie $bowtie_version binaries\n\n";
-        if($a =~ /Darwin/i){ ## download mac version
-            $bowtie = "bowtie-$bowtie_version-macos-x86_64.zip";
-        }elsif($a =~ /x86_64/i){
-            $bowtie = "bowtie-$bowtie_version-linux-x86_64.zip";
-        }else{
-            $bowtie = "bowtie-$bowtie_version-src.zip";
-        }
-        
-        if(not -f $bowtie){
-	    if(check("http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/$bowtie_version/$bowtie")){
-		$err=system("$dtool http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/$bowtie_version/$bowtie $dopt");
-		
-		if($err){
-		    die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
+	if(not -d "bowtie-$bowtie_version"){
+		## this needed to be added cause the authors removed the 0 in the version number for the filename
+
+
+		print STDERR "Downloading bowtie $bowtie_version binaries\n\n";
+		if($a =~ /Darwin/i){ ## download mac version
+			$bowtie = "bowtie-$bv-macos-x86_64.zip";
+		}elsif($a =~ /x86_64/i){
+			$bowtie = "bowtie-$bv-linux-x86_64.zip";
+		}else{
+			$bowtie = "bowtie-$bv-src.zip";
+		}
+
+		if(not -f $bowtie){
+			if(check("http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/$bowtie_version/$bowtie")){
+				$err=system("$dtool http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/$bowtie_version/$bowtie $dopt");
+
+				if($err){
+					die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
+				}
+			}elsif(check("http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/old/$bowtie_version/$bowtie")){
+				$err=system("$dtool http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/old/$bowtie_version/$bowtie $dopt");
+				if($err){
+					die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
+				}
+			}elsif(check("https://sourceforge.net/projects/bowtie-bio/files/bowtie/$bowtie_version/$bowtie")){
+				$err=system("$dtool https://sourceforge.net/projects/bowtie-bio/files/bowtie/$bowtie_version/$bowtie $dopt");
+				if($err){
+					die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
+				}
+
+			}else{
+				die "\nError:\n\t$bowtie not found on server http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/ \n\n\n";
+			}
+		}
+
+		if(not -f "$bowtie"){
+			die "$bowtie download failed \nPlease try to download bowtie manually from here http://bowtie-bio.sourceforge.net/index.shtml";
 		}
-            }elsif(check("http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/old/$bowtie_version/$bowtie")){
-		$err=system("$dtool http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/old/$bowtie_version/$bowtie $dopt");
+
+		print STDERR "Installing bowtie binaries\n\n";
+		$err=system("unzip -u $bowtie 1>> install.log 2>>install_error.log");
+
 		if($err){
-		    die "\nError:\n\t$bowtie could not be downloaded\n\n\n";
+			die "unzip $bowtie was not successful\n";
 		}
-	    }else{
-		die "\nError:\n\t$bowtie not found on server http://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie/ \n\n\n";
-	    }
-        }
-        
-        if(not -f "$bowtie"){
-            die "$bowtie download failed \nPlease try to download bowtie manually from here http://bowtie-bio.sourceforge.net/index.shtml";
-        }
-                
-        print STDERR "Installing bowtie binaries\n\n";
-        $err=system("unzip -u $bowtie 1>> install.log 2>>install_error.log");
-        
-        if($err){
-            die "unzip $bowtie was not successful\n";
-        }
-    }
-			
-    #$in = `$grep "$dir/essentials/bowtie-$bowtie_version:*" ~/.bashrc` if(-f "~/.bashrc");
-    #if(not $in){
-    #    `echo 'export PATH=\$PATH:$dir/essentials/bowtie-$bowtie_version' >> ~/.bashrc`;
-    #}
-
-    #$in = `$grep "$dir/essentials/bowtie-$bowtie_version:*" ~/$shellconf`;
-    #if(not $in){
-    #    `echo 'export PATH=\$PATH:$dir/essentials/bowtie-$bowtie_version' >> ~/$shellconf`;
-    #}
-
-
-    #$in2 = `$grep "$dir/essentials/bowtie-$bowtie_version:*" ~/.cshrc` if(-f "~/.cshrc");
-    #
-    #if(not $in2){
-    #    `echo 'setenv PATH \$PATH:$dir/essentials/bowtie-$bowtie_version' >> ~/.cshrc`;
-    #}
-    chdir "$install_bin_dir";
-	
-	buildgood("$dir/essentials/bowtie-$bowtie_version/bowtie");
-	
+	}
+
+	chdir "$install_bin_dir";
+
+	buildgood("$dir/essentials/bowtie-$bv/bowtie");
+
 	if(not -f "bowtie"){
-    system("ln -s $dir/essentials/bowtie-$bowtie_version/bowtie* .");
-}
-    chdir "$dir/essentials/";
+		system("ln -s $dir/essentials/bowtie-$bv/bowtie* .");
+	}
+	chdir "$dir/essentials/";
 
 }
 
-$ret = checkBIN("RNAfold -h 2","usage");
-#my $rna_inst=`RNAfold 2>&1`;
+$ret = checkBIN("RNAfold -h","usage");
 
-#if($rna_inst !~ /no\s*RNAfold/i){
 if($ret == 0){
-   print STDERR "RNAfold                                          already installed, nothing to do ...\n";
-   $progs{RNAfold}=1;
+	print STDERR "RNAfold                                          already installed, nothing to do ...\n";
+	$progs{RNAfold}=1;
 }else{
-    if(not -d "ViennaRNA-1.8.4"){
-        $dfile="ViennaRNA-1.8.4.tar.gz";
-        if(not -f $dfile){
-            print STDERR "Downloading Vienna package now\n\n";
+	if(not -d "ViennaRNA-1.8.4"){
+		$dfile="ViennaRNA-1.8.4.tar.gz";
+		if(not -f $dfile){
+			print STDERR "Downloading Vienna package now\n\n";
 			if(check("http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-1.8.4.tar.gz")){
 				$err=system("$dtool http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-1.8.4.tar.gz $dopt");
 				if($err){
@@ -330,53 +324,52 @@
 				}
 			}else{
 				die "Vienna package not found at  http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-1.8.4.tar.gz
-                Please try to download the Vienna package from here http://www.tbi.univie.ac.at/RNA/RNAfold.html 
-\n";
+				Please try to download the Vienna package from here http://www.tbi.univie.ac.at/RNA/RNAfold.html 
+				\n";
 			}
+		}
+
+		if(not -f "ViennaRNA-1.8.4.tar.gz"){
+			die "Vienna package download failed\n";
+		}
 	}
-        
-        
-        if(not -f "ViennaRNA-1.8.4.tar.gz"){
-            die "Vienna package download failed\n";
-        }
-    }
-
-    if(not -f "ViennaRNA-1.8.4/Progs/RNAfold"){
-	print STDERR "Installing Vienna package now \n\n";
-	`tar xzf ViennaRNA-1.8.4.tar.gz`;
-	chdir("ViennaRNA-1.8.4/");
-	chdir("lib");
-	
-	open IN,"<fold.c" or die "File fold.c not found\n";
-	open OUT,">fold.c.new" or die "Cannot generate file fold.c.new\n";
-	while(<IN>){
-	    if(/inline\s+(int\s+LoopEnergy.+$)/i){
-		print OUT "$1";
-	    }elsif(/^inline\s+(int\s+HairpinE.+$)/i){
-		print OUT "$1";
-	    }else{
-		print OUT;
-	    }
-	}
-	close OUT;
-    
-	`mv fold.c fold.c.orig`;
-	`mv fold.c.new fold.c`;
-	chdir("..");
-    
-	`./configure --prefix=$dir/essentials/ViennaRNA-1.8.4/install_dir`;
-	`make 1>> ../install.log 2>> ../install_error.log`;
-	`make install 1>> ../install.log 2>> ../install_error.log`;
 
-	buildgood("$dir/essentials/ViennaRNA-1.8.4/install_dir/bin/RNAfold");
+	if(not -f "ViennaRNA-1.8.4/Progs/RNAfold"){
+		print STDERR "Installing Vienna package now \n\n";
+		`tar xzf ViennaRNA-1.8.4.tar.gz`;
+		chdir("ViennaRNA-1.8.4/");
+		chdir("lib");
 
-	chdir("..");
-	chdir "$install_bin_dir";
-	if(not -f "RNAfold"){
-		system("ln -s $dir/essentials/ViennaRNA-1.8.4/install_dir/bin/RNAfold .");
+		open IN,"<fold.c" or die "File fold.c not found\n";
+		open OUT,">fold.c.new" or die "Cannot generate file fold.c.new\n";
+		while(<IN>){
+			if(/inline\s+(int\s+LoopEnergy.+$)/i){
+				print OUT "$1";
+			}elsif(/^inline\s+(int\s+HairpinE.+$)/i){
+				print OUT "$1";
+			}else{
+				print OUT;
+			}
+		}
+		close OUT;
+
+		`mv fold.c fold.c.orig`;
+		`mv fold.c.new fold.c`;
+		chdir("..");
+
+		`./configure --prefix=$dir/essentials/ViennaRNA-1.8.4/install_dir`;
+		`make 1>> ../install.log 2>> ../install_error.log`;
+		`make install 1>> ../install.log 2>> ../install_error.log`;
+
+		buildgood("$dir/essentials/ViennaRNA-1.8.4/install_dir/bin/RNAfold");
+
+		chdir("..");
+		chdir "$install_bin_dir";
+		if(not -f "RNAfold"){
+			system("ln -s $dir/essentials/ViennaRNA-1.8.4/install_dir/bin/RNAfold .");
+		}
+		chdir "$dir/essentials/"	
 	}
-	chdir "$dir/essentials/"	
-    }
 }
 
 #$in = `$grep "$dir/essentials/ViennaRNA-1.8.4/install_dir/bin:*" ~/.bashrc`;
@@ -395,7 +388,7 @@
 
 #$in2 = `$grep "$dir/essentials/ViennaRNA-1.8.4/install_dir/bin:*" ~/.cshrc`;
 #if(not $in2){
-    #`echo 'setenv PATH \$PATH:$dir/essentials/ViennaRNA-1.8.4/install_dir/bin' >> ~/.cshrc`;
+#`echo 'setenv PATH \$PATH:$dir/essentials/ViennaRNA-1.8.4/install_dir/bin' >> ~/.cshrc`;
 #}
 
 
@@ -407,104 +400,104 @@
 
 #if($randf =~ /no\s*randfold/i){ ## this should work
 if($ret == 0){
-    print STDERR "randfold\t\t\t\t\t already installed, nothing to do ...\n";
+	print STDERR "randfold\t\t\t\t\t already installed, nothing to do ...\n";
 	$progs{randfold}=1;
 }else{
 
-    $dfile="squid-1.9g.tar.gz";
-    if(not -f $dfile){
-        print STDERR "Downloading SQUID library now\n\n";
-        `$dtool http://eddylab.org/software/squid/squid.tar.gz $dopt`;
+	$dfile="squid-1.9g.tar.gz";
+	if(not -f $dfile){
+		print STDERR "Downloading SQUID library now\n\n";
+		`$dtool http://eddylab.org/software/squid/squid.tar.gz $dopt`;
 		`mv squid.tar.gz $dfile`;
-    }
-    if(not -f $dfile){
+	}
+	if(not -f $dfile){
 		system("cp ../squid-1.9g.tar.gz squid-1.9g.tar.gz");
-    }
-	
-    if(not -f "squid-1.9g.tar.gz"){
-        die "squid could not be downloaded\n Please try to download the library from here http://selab.janelia.org/software.html";
-    }
-
-    if(not -d "squid-1.9g" and -f "squid-1.9g.tar.gz"){
-        print STDERR "Extracting squid and configuring it now\n\n"; 
-        `mkdir squid-1.9g`;
+	}
+
+	if(not -f "squid-1.9g.tar.gz"){
+		die "squid could not be downloaded\n Please try to download the library from here http://selab.janelia.org/software.html";
+	}
+
+	if(not -d "squid-1.9g" and -f "squid-1.9g.tar.gz"){
+		print STDERR "Extracting squid and configuring it now\n\n"; 
+		`mkdir squid-1.9g`;
 		`tar xzf squid-1.9g.tar.gz -C squid-1.9g`;
 		my $a=`ls squid-1.9g`;
 		chomp $a;
 		`mv squid-1.9g/$a/* squid-1.9g/`;
 		`rm -rf squid-1.9g/$a`;
-				
+
 		chdir("squid-1.9g");
-        `./configure 1>>../install.log 2>>../install_error.log`;
-        `make 1>>../install.log 2>>install_error.log`;
+		`./configure 1>>../install.log 2>>../install_error.log`;
+		`make 1>>../install.log 2>>install_error.log`;
 
 		buildgood("$dir/essentials/squid-1.9g/libsquid.a");
 
-        chdir("..");
-    }
+		chdir("..");
+	}
 
 	$dfile="randfold-2.0.tar.gz";
-    if(not -f $dfile ){
-        print STDERR "Downloading randfold now\n\n";
-        `$dtool http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz $dopt`;
-    }
-
-    if(not -f "randfold-2.0.tar.gz"){
-        die "randfold could not be downloaded\nPlease try to download randfold from here http://bioinformatics.psb.ugent.be/software/details/Randfold\n";
-    }
-
-    if(not -d "randfold-2.0" and -f "randfold-2.0.tar.gz"){
-        print STDERR "Installing randfold now\n\n";
-        `tar xzf randfold-2.0.tar.gz`;
-        
-        chdir("randfold-2.0");
-
-        open IN,"<Makefile" or die "File Makefile not found\n\n";
-        open OUT,">Makefile_new" or die "Makefile_new could not be created\n\n";
-
-        while(<IN>){
-            if(/INCLUDE=-I\.\s*/i){
-                print OUT "INCLUDE=-I. -I$dir/essentials/squid-1.9g -L$dir/essentials/squid-1.9g/\n";
-            }else{
-                print OUT;
-            }
-        }
-        close IN;
-        close OUT;
-
-	## added so we can make it run on MacOSX as well.
-	
-	open IN,"<fold.c" or die "File fold.c not found\n";
-	open OUT,">fold.c.new" or die "Cannot generate file fold.c.new\n";
-	while(<IN>){
-	    if(/^inline\s+(int\s+LoopEnergy.+$)/i){
-		print OUT "$1";
-	    }elsif(/^inline\s+(int\s+HairpinE.+$)/i){
-		print OUT "$1";
-	    }else{
-		print OUT;
-	    }
-	}
-	close OUT;
-	
-
-        `mv fold.c fold.c.orig`;
-        `mv fold.c.new fold.c`;
-	
-        `mv Makefile Makefile.orig`;
-        `mv Makefile_new Makefile`;
-
-        `make 1>>../install.log 2>>../install_error.log`;
-         buildgood("$dir/essentials/randfold-2.0/randfold");
-         chdir("..");
-    }
+	if(not -f $dfile ){
+		print STDERR "Downloading randfold now\n\n";
+		`$dtool http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz $dopt`;
+	}
+
+	if(not -f "randfold-2.0.tar.gz"){
+		die "randfold could not be downloaded\nPlease try to download randfold from here http://bioinformatics.psb.ugent.be/software/details/Randfold\n";
+	}
+
+	if(not -d "randfold-2.0" and -f "randfold-2.0.tar.gz"){
+		print STDERR "Installing randfold now\n\n";
+		`tar xzf randfold-2.0.tar.gz`;
+
+		chdir("randfold-2.0");
+
+		open IN,"<Makefile" or die "File Makefile not found\n\n";
+		open OUT,">Makefile_new" or die "Makefile_new could not be created\n\n";
+
+		while(<IN>){
+			if(/INCLUDE=-I\.\s*/i){
+				print OUT "INCLUDE=-I. -I$dir/essentials/squid-1.9g -L$dir/essentials/squid-1.9g/\n";
+			}else{
+				print OUT;
+			}
+		}
+		close IN;
+		close OUT;
+
+		## added so we can make it run on MacOSX as well.
+
+		open IN,"<fold.c" or die "File fold.c not found\n";
+		open OUT,">fold.c.new" or die "Cannot generate file fold.c.new\n";
+		while(<IN>){
+			if(/^inline\s+(int\s+LoopEnergy.+$)/i){
+				print OUT "$1";
+			}elsif(/^inline\s+(int\s+HairpinE.+$)/i){
+				print OUT "$1";
+			}else{
+				print OUT;
+			}
+		}
+		close OUT;
+
+
+		`mv fold.c fold.c.orig`;
+		`mv fold.c.new fold.c`;
+
+		`mv Makefile Makefile.orig`;
+		`mv Makefile_new Makefile`;
+
+		`make 1>>../install.log 2>>../install_error.log`;
+		buildgood("$dir/essentials/randfold-2.0/randfold");
+		chdir("..");
+	}
 
 #    $in = `$grep "$dir/essentials/randfold-2.0:*" ~/.bashrc`;
 #    if(not $in){ 
 #        print STDERR "Randfold path has been added to \$PATH variable\n"; 
 #        `echo 'export PATH=\$PATH:$dir/essentials/randfold-2.0' >> ~/.bashrc`;
 #    }
-    
+
 #    $in = `$grep "$dir/essentials/randfold-2.0:*" ~/$shellconf`;
 #    if(not $in){ 
 #        print STDERR "Randfold path has been added to \$PATH variable\n"; 
@@ -514,11 +507,11 @@
 
 #    $in2 = `$grep "$dir/essentials/randfold-2.0:*" ~/.cshrc`;
 #    if($in2){
-        #`echo 'setenv PATH \$PATH:$dir/essentials/randfold-2.0' >> ~/.cshrc`;
-    #    }
-    chdir "$install_bin_dir";
+	#`echo 'setenv PATH \$PATH:$dir/essentials/randfold-2.0' >> ~/.cshrc`;
+	#    }
+	chdir "$install_bin_dir";
 	if(not -f "randfold"){
-         system("ln -s $dir/essentials/randfold-2.0/randfold .");
+		system("ln -s $dir/essentials/randfold-2.0/randfold .");
 	}
 	chdir "$dir/essentials/"
 }
@@ -528,10 +521,10 @@
 my $zlib=`perl -e 'use Compress::Zlib;' 2>&1`;
 
 if(not $zlib){
-    print STDERR "Compress::Zlib\t\t\t\t\t already installed, nothing to do ...\n";
+	print STDERR "Compress::Zlib\t\t\t\t\t already installed, nothing to do ...\n";
 	$progs{zlib}=1;
 }else{
-    die "please install Compress::Zlib by using CPAN before you proceed\n";
+	die "please install Compress::Zlib by using CPAN before you proceed\n";
 
 }
 
@@ -541,38 +534,38 @@
 $ret = checkBIN("perl -e \'use Font::TTF; print \"installed\";\'","installed");
 
 if($ret == 0){
-    print STDERR "Font::TTf                                        already installed, nothing to do ...\n";
+	print STDERR "Font::TTf                                        already installed, nothing to do ...\n";
 	$progs{ttf}=1;
 }else{
-    my $version='';
-    `$dtool http://www.cpan.org/authors/id/M/MH/MHOSKEN/CHECKSUMS $dopt`;
-    open IN,"CHECKSUMS" or die "File checksums not found\n";
-    while(<IN>){
-	if(/((Font-TTF-\d.+).tar.gz)/){
-	    $dfile=$1;
-	    $version=$2;
-	}
-    }
-    close IN;
-    
-    if(not -f $dfile){
-        print STDERR "Downloading Font::TTF now\n\n";
-        `$dtool http://www.cpan.org/authors/id/M/MH/MHOSKEN/$dfile $dopt`;
-    }
-
-    if(not -f $dfile){
-        die "Download of Font::TTF failed\n\n";
-    }
-
-        print STDERR "Installing Font-TTF now\n\n";
-        `tar xzf $dfile`; 
-        chdir("$version");
-        
+	my $version='';
+	`$dtool http://www.cpan.org/authors/id/M/MH/MHOSKEN/CHECKSUMS $dopt`;
+	open IN,"CHECKSUMS" or die "File checksums not found\n";
+	while(<IN>){
+		if(/((Font-TTF-\d.+).tar.gz)/){
+			$dfile=$1;
+			$version=$2;
+		}
+	}
+	close IN;
+
+	if(not -f $dfile){
+		print STDERR "Downloading Font::TTF now\n\n";
+		`$dtool http://www.cpan.org/authors/id/M/MH/MHOSKEN/$dfile $dopt`;
+	}
+
+	if(not -f $dfile){
+		die "Download of Font::TTF failed\n\n";
+	}
+
+	print STDERR "Installing Font-TTF now\n\n";
+	`tar xzf $dfile`; 
+	chdir("$version");
+
 	`perl Makefile.PL INSTALL_BASE=$ENV{'HOME'}/perl5 LIB=$dir/lib/perl5`;
 	`make 1>>../install.log 2>>../install_error.log`;
 
 	`mv Makefile Makefile.orig`;
-	
+
 	open IN,"Makefile.orig" or die "No Makefile found\n";
 	open OUT,">Makefile" or die "No Makefile found\n";
 	while(my $cl= <IN>){
@@ -585,14 +578,14 @@
 	close IN;
 
 	`make install 1>>../install.log 2>>..install_error.log`;
-	
+
 	$ret = checkBIN("perl -e \'use Font::TTF; print \"installed\";\'","installed");
 
 	if($ret == 0){
-    print STDERR "Font::TTF                                        installation successful \n";
-	$progs{ttf}=1;
-}	
-	
+		print STDERR "Font::TTF                                        installation successful \n";
+		$progs{ttf}=1;
+	}	
+
 	chdir("..");
 }
 
@@ -601,37 +594,37 @@
 $ret = checkBIN("perl -e \'use PDF::API2; print \"installed\";\'","installed");
 
 if($ret == 0){
-    print STDERR "PDF::API2                                        already installed, nothing to do ...\n";
+	print STDERR "PDF::API2                                        already installed, nothing to do ...\n";
 	$progs{pdf}=1;
 }else{
-    my $version='';
-    `$dtool http://www.cpan.org/authors/id/S/SS/SSIMMS/CHECKSUMS $dopt`;
-    open IN,"CHECKSUMS" or die "File checksums not found\n";
-    while(<IN>){
-	if(/((PDF-API2.+).tar.gz)/){
-	    $dfile=$1;
-	    $version=$2;
-	}
-    }
-    close IN;
-    
-    if(not -f $dfile){
-        print STDERR "Downloading PDF-API2 now\n\n";
-        `$dtool http://ftp-stud.hs-esslingen.de/pub/Mirrors/CPAN/authors/id/S/SS/SSIMMS/$dfile $dopt`;
-    }
-
-    if(not -f $dfile){
-        die "Download of PDF-API2 failed\n\n";
-    }
-
-        print STDERR "Installing PDF-API2 now\n\n";
-        `tar xzf $dfile`; 
-        chdir("$version");
-        
+	my $version='';
+	`$dtool http://www.cpan.org/authors/id/S/SS/SSIMMS/CHECKSUMS $dopt`;
+	open IN,"CHECKSUMS" or die "File checksums not found\n";
+	while(<IN>){
+		if(/((PDF-API2.+).tar.gz)/){
+			$dfile=$1;
+			$version=$2;
+		}
+	}
+	close IN;
+
+	if(not -f $dfile){
+		print STDERR "Downloading PDF-API2 now\n\n";
+		`$dtool http://ftp-stud.hs-esslingen.de/pub/Mirrors/CPAN/authors/id/S/SS/SSIMMS/$dfile $dopt`;
+	}
+
+	if(not -f $dfile){
+		die "Download of PDF-API2 failed\n\n";
+	}
+
+	print STDERR "Installing PDF-API2 now\n\n";
+	`tar xzf $dfile`; 
+	chdir("$version");
+
 	`perl Makefile.PL INSTALL_BASE=$ENV{'HOME'}/perl5 LIB=$dir/lib/perl5`;
 	`make 1>>../install.log 2>>..install_error.log`;
 	`mv Makefile Makefile.orig`;
-	
+
 	open IN,"Makefile.orig" or die "No Makefile found\n";
 	open OUT,">Makefile" or die "No Makefile found\n";
 	while(my $cl= <IN>){
@@ -644,12 +637,12 @@
 	close IN;
 
 	`make install 1>>../install.log 2>>..install_error.log`;
-		
+
 	$ret = checkBIN("perl -e \'use PDF::API2; print \"installed\";\'","installed");
 
 	if($ret == 0){
 		print STDERR "PDF::API2                                        installation successful\n";
-	    $progs{pdf}=1;
+		$progs{pdf}=1;
 	}
 
 	chdir("..");
@@ -662,21 +655,21 @@
 }
 
 if($sum == 6){
-  print STDERR "\n\nInstallation successful\n\n\n\n\n\n";
-  print STDERR "To check if everything works fine you can now change to the 
-tutorial_dir and type 'bash run_tut.sh' to make a test run\n\n";
-  
-  chdir $dir;
-  open EF,">install_successful" or die "Could not create file install_successful\n
-  In case that all tools are running properly then please create this empty file manually 
-  in your mirdeep2 installation folder. Otherwise the other tools will not run.
-  ";
-  close EF;
+	print STDERR "\n\nInstallation successful\n\n\n\n\n\n";
+	print STDERR "To check if everything works fine you can now change to the 
+	tutorial_dir and type 'bash run_tut.sh' to make a test run\n\n";
+
+	chdir $dir;
+	open EF,">install_successful" or die "Could not create file install_successful\n
+	In case that all tools are running properly then please create this empty file manually 
+	in your mirdeep2 installation folder. Otherwise the other tools will not run.
+	";
+	close EF;
 }else{
 	print STDERR "\n\nPlease run the install.pl script again to check if 
-everything is properly installed.
+	everything is properly installed.
 
-";
+	";
 }
 
 
@@ -684,81 +677,93 @@
 
 
 sub rem_mirdeep{
-    my ($file)=@_;
-    if(-f "$ENV{'HOME'}/$file"){
-        `cp ~/$file ~/${file}_$time`;
-        print STDERR "~/$file backup is ~/${file}_$time\n";
-        `mv ~/$file ~/$file.bak`;
-        open OUT,">$ENV{'HOME'}/$file" or die "Cannot create file $ENV{'HOME'}/$file\n";
-        open IN,"$ENV{'HOME'}/$file.bak";
-        my @line;
-        my $tmp;
-        while(<IN>){
-            $tmp="";
-            if(/mirdeep/){
-                @line = split(/:/);
-                foreach(@line){
-                    if(/mirdeep/){}else{
-                        $tmp.="$_";
-                    }
-                }
-                if($file !~ /.cshrc/){
-                    
-                    if($tmp !~ /PATH=\$PATH$/ and $tmp !~ /PERL5LIB=\$PERL5LIB\s*$/){
-                        print OUT "$tmp\n";
-                    }
-                }else{
-                    if($tmp !~ /PATH \$PATH$/ and $tmp !~ /PERL5LIB \$PERL5LIB\s*$/){
-                        print OUT "$tmp\n";
-                    }
-                }
-            }else{
-                print OUT;
-            }
-        }
-    }else{
-        print "file $ENV{'HOME'}/$file.bak not found\n";
-    }
+	my ($file)=@_;
+	if(-f "$ENV{'HOME'}/$file"){
+		`cp ~/$file ~/${file}_$time`;
+		print STDERR "~/$file backup is ~/${file}_$time\n";
+		`mv ~/$file ~/$file.bak`;
+		open OUT,">$ENV{'HOME'}/$file" or die "Cannot create file $ENV{'HOME'}/$file\n";
+		open IN,"$ENV{'HOME'}/$file.bak";
+		my @line;
+		my $tmp;
+		while(<IN>){
+			$tmp="";
+			if(/mirdeep/){
+				@line = split(/:/);
+				foreach(@line){
+					if(/mirdeep/){}else{
+						$tmp.="$_";
+					}
+				}
+				if($file !~ /.cshrc/){
+
+					if($tmp !~ /PATH=\$PATH$/ and $tmp !~ /PERL5LIB=\$PERL5LIB\s*$/){
+						print OUT "$tmp\n";
+					}
+				}else{
+					if($tmp !~ /PATH \$PATH$/ and $tmp !~ /PERL5LIB \$PERL5LIB\s*$/){
+						print OUT "$tmp\n";
+					}
+				}
+			}else{
+				print OUT;
+			}
+		}
+	}else{
+		print "file $ENV{'HOME'}/$file.bak not found\n";
+	}
 }
 
 
 sub checkBIN{
-    my ($a,$b) = @_;    
+	my ($a,$b) = @_;    
 	my $e = system("$a> tmp 2>tmp2");
-	
-    open IN,"<tmp";
-    my $found =1;
-    while(<IN>){
-		if(/$b/){
+
+	open IN,"<tmp";
+	my $found =1;
+	while(<IN>){
+		if(/$b/i){
 			$found =0;
-			
+
 		}
 	}
 	close IN;
 	if($found){
 		open IN,"<tmp2";
 		while(<IN>){
-			if(/$b/){
+			if(/$b/i){
 				$found =0;
-				
+
 			}
 		}
 	}
-    close IN;
-    return $found;
+	close IN;
+	return $found;
 }
 
 
-## this routine checks if files exists on remote servers
 sub check{
 	my ($url) = @_;
-	if (head($url)) {
-		return 1;
+	my $out='';
+	if($dtool =~ /wget/){
+		$out=`wget --spider -v $url 2>&1`;
+	}elsif($dtool =~ /curl/){
+		$out=`curl --head $url |head -n1`;
+		if($out =~ /NOT/i){
+			$out='broken';
+		}
 	}else{
+		die "No download tool found\nplease install wget or curl\n";
+	}
+
+	if($out =~ /broken/){
 		return 0;
+	}else{
+		return 1;
 	}
 }
 
+
 sub buildgood{
 	if(-f $_[0]){
 		print STDERR "Building of $_[0] successful\n";