--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/install.pl	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,316 @@
+#!/usr/bin/perl
+
+=head1 NAME
+   install.pl
+
+=head1 SYNOPSIS
+    USAGE: install.pl --prefix=/location/of/install/dir
+
+=head1 OPTIONS
+
+B<--prefix, -p>
+	Required. Prefix location where package will be installed.
+
+B<--perl_exec, -e>
+	Optional.  If perl exec is other than /usr/bin/perl please specify location of perl install
+
+B<--help,-h>
+
+
+=head1  DESCRIPTION
+	Install package
+
+=head1  INPUT
+
+=head1  OUTPUT
+
+
+=head1  CONTACT
+  bjaysheel@gmail.com
+
+
+==head1 EXAMPLE
+	./install.pl --prefix=/prefix
+
+=cut
+
+use strict;
+use warnings;
+use Cwd;
+use Data::Dumper;
+use Pod::Usage;
+use Getopt::Long qw(:config no_ignore_case no_auto_abbrev pass_through);
+
+my %options = ();
+my $results = GetOptions (\%options,
+                          'prefix|p=s',
+						  'perl_exec|e=s',
+						  'help|h') || pod2usage();
+
+## display documentation
+if( $options{'help'} ){
+    pod2usage( {-exitval => 0, -verbose => 2, -output => \*STDERR} );
+}
+
+#############################################################################
+#### make sure everything passed was peachy
+&check_parameters(\%options);
+
+#### print time now.
+timestamp();
+
+my $this = {};
+my $progress = {};
+my $cmd = "";
+
+#### get current working dir
+$this->{source} = getcwd();
+
+$progress = getProgress();
+
+#### make logs dir
+$cmd = "mkdir -p $options{prefix}/logs";
+execute_cmd($cmd);
+
+#### installling libraries required for successfull run
+install_libraries();
+
+#### unpack binary dir containing all binary to be installed
+#### which are required for successfull run
+print STDERR "\n\nInstalling binaries...\n";
+
+#### install each package in binary folder.
+my @packages = qw(stringApprox levD);
+
+foreach my $tool (@packages) {
+	if ((exists $progress->{$tool}) && ($progress->{$tool})){
+		print STDERR "\t$tool already installed. Skipping...\n";
+	} else {
+		print STDERR "\tInstalling $tool...\n";
+
+		#### unpack and install each tool
+		eval("install_${tool}()");
+	}
+}
+
+#### copy source code and update paths for perl and libs
+install_source();
+
+#### completion message
+print "\n\n\tSoftSearch installation complete.  Use following command to initiate a test run\n";
+print "\n\tperl $options{prefix}/src/SoftSearch.pl -f {GENOME} -b {BAM_FILE}\n\n";
+
+#### print time now
+timestamp();
+
+#############################################################################
+sub check_parameters {
+    my $options = shift;
+
+	my @required = qw(prefix);
+
+	foreach my $key (@required) {
+		unless ($options{$key}) {
+			print STDERR "ARG: $key is required\n";
+			pod2usage({-exitval => 2,  -message => "error message", -verbose => 1, -output => \*STDERR});
+			exit(-1);
+		}
+	}
+
+	$options{'perl_exec'} = "/usr/bin/perl" unless($options{'perl_exec'});
+}
+
+#############################################################################
+sub getProgress {
+	my $hash = {};
+	my @sofar;
+
+	#### if file exists get progress so far.
+	if (-s "$options{prefix}/progress.txt") {
+		open(FHD, "<", "$options{prefix}/progress.txt") or die "Could not open file to read $options{prefix}/progress.txt";
+		while(<FHD>){
+			chomp $_;
+			push @sofar, $_;
+		}
+		close(FHD);
+
+		map { $hash->{$1} = $2 if( /([^=]+)\s*=\s*([^=]+)/ ) } @sofar;
+	}
+
+	#### return hash
+	return $hash;
+}
+
+#############################################################################
+sub setProgress {
+	my $hash = shift;
+
+	open(OUT, ">", "$options{prefix}/progress.txt") or die "Could not open file to write $options{prefix}/progress.txt";
+
+	foreach my $key (keys %{$hash}){
+		print OUT $key."=".$hash->{$key}."\n";
+	}
+
+	close(OUT);
+}
+
+#############################################################################
+sub install_libraries {
+	if ((exists $progress->{libraries}) && ($progress->{libraries})){
+		print STDERR "\tLibraries already installed. Skipping...\n";
+		return;
+	}
+
+	print STDERR "\n\nInstalling libraries...\n\n";
+	chdir($this->{source});
+
+	$cmd = "cp -r $this->{source}/library $options{prefix}/lib";
+	execute_cmd($cmd);
+
+	$progress->{libraries} = 1;
+	setProgress($progress);
+}
+
+#############################################################################
+sub install_stringApprox {
+	#### check and install dir
+	my $dir = "$options{prefix}/lib";
+	my $cmd = "";
+
+	$cmd = "mkdir -p $dir";
+	execute_cmd($cmd);
+
+	$cmd = "tar -zxvf $this->{source}/binary/String-Approx-3.27.tar.gz -C $this->{source}/binary";
+	execute_cmd($cmd);
+
+	chdir("$this->{source}/binary/String-Approx-3.27");
+	$cmd = "perl Makefile.PL INSTALL_BASE=$options{prefix}";
+	$cmd .= " 1>$options{prefix}/logs/StringApprox.out";
+	$cmd .= " 2>$options{prefix}/logs/StringApprox.err";
+	execute_cmd($cmd);
+
+	$cmd = "make && make install";
+	$cmd .= " 1>>$options{prefix}/logs/StringApprox.out";
+	$cmd .= " 2>>$options{prefix}/logs/StringApprox.err";
+	execute_cmd($cmd);
+
+	$cmd = "make install";
+	$cmd .= " 1>>$options{prefix}/logs/StringApprox.out";
+	$cmd .= " 2>>$options{prefix}/logs/StringApprox.err";
+	execute_cmd($cmd);
+
+
+	chdir("$this->{source}/binary");
+	$cmd = "rm -rf $this->{source}/binary/String-Approx-3.27";
+	execute_cmd($cmd);
+
+	$progress->{stringApprox} = 1;
+	setProgress($progress);
+}
+
+#############################################################################
+sub install_levD {
+	#### check and install dir
+	my $dir = "$options{prefix}/lib";
+	my $cmd = "";
+
+	$cmd = "mkdir -p $dir";
+	execute_cmd($cmd);
+
+	$cmd = "tar -zxvf $this->{source}/binary/Text-LevenshteinXS-0.03.tar.gz -C $this->{source}/binary";
+	execute_cmd($cmd);
+
+	chdir("$this->{source}/binary/Text-LevenshteinXS-0.03");
+	$cmd = "perl Makefile.PL INSTALL_BASE=$options{prefix}";
+	$cmd .= " 1>$options{prefix}/logs/levD.out";
+	$cmd .= " 2>$options{prefix}/logs/levD.err";
+	execute_cmd($cmd);
+
+	$cmd = "make";
+	$cmd .= " 1>>$options{prefix}/logs/levD.out";
+	$cmd .= " 2>>$options{prefix}/logs/levD.err";
+	execute_cmd($cmd);
+
+	$cmd .= "make install";
+	$cmd .= " 1>>$options{prefix}/logs/levD.out";
+	$cmd .= " 2>>$options{prefix}/logs/levD.err";
+	execute_cmd($cmd);
+
+	chdir("$this->{source}/binary");
+	$cmd = "rm -rf $this->{source}/binary/Text-LevenshteinXS-0.03";
+	execute_cmd($cmd);
+
+	$progress->{levD} = 1;
+	setProgress($progress);
+}
+
+#############################################################################
+sub install_source {
+	if ((exists $progress->{source}) && ($progress->{source})){
+		print STDERR "\tSource already installed. Skipping...\n";
+		return;
+	}
+
+	print STDERR "\n\nInstalling source...\n\n";
+
+	#### create dir to store source code
+	$cmd = "mkdir -p $options{prefix}/src";
+	execute_cmd($cmd);
+
+	$cmd = "cp -r $this->{source}/script/* $options{prefix}/src/.";
+	execute_cmd($cmd);
+
+	#### make sure all scripts are executable
+	$cmd = "chmod -R +x $options{prefix}/src";
+	execute_cmd($cmd);
+
+	#### replace /usr/local/biotools/perl/5.10.0/bin/perl with perl_exec
+	$options{perl_exec} =~ s/\//\\\//g;
+	$cmd = "find $options{prefix}/src -name \"*.pl\" -print";
+	$cmd .= " -exec sed -i 's/#!\\/usr\\/local\\/biotools\\/perl\\/5.10.0\\/bin\\/perl/#!$options{perl_exec}/' {} \\;";
+	execute_cmd($cmd);
+
+	#### check if perl exec location is other than /usr/bin/perl
+	if ($options{perl_exec} !~ /^\/usr\/bin\/perl$/) {
+		$cmd = "find $options{prefix}/src -name \"*.pl\" -print";
+		$cmd .= " -exec sed -i 's/#!\\/usr\\/bin\\/perl/#!$options{perl_exec}/' {} \\;";
+		execute_cmd($cmd);
+	}
+
+	#### replace library references to local install
+	my $lib = "$options{prefix}/lib";
+	$lib =~ s/\//\\\//g;
+
+        $cmd = "find $options{prefix}/src -name \"*.pl\" -print";
+        $cmd .= " -exec sed -i 's/\\/data2\\/bsi\\/reference\\/softsearch\\/lib/$lib/' {} \\;";
+        execute_cmd($cmd);
+        
+        $cmd = "find $options{prefix}/lib -name \"LevD.pm\" -print";
+        $cmd .= " -exec sed -i 's/\\/data2\\/bsi\\/reference\\/softsearch\\/lib/$lib/' {} \\;";
+        execute_cmd($cmd);
+
+	$progress->{source} = 1;
+	setProgress($progress);
+}
+
+#############################################################################
+sub execute_cmd {
+	my $cmd = shift;
+
+	system($cmd);
+
+	#while (( $? >> 8 ) != 0 ){
+	#	print STDERR "ERROR: Following command failed to execute. Exiting execution of workflow\n$cmd\n";
+	#	exit(-1);
+	#}
+}
+
+#############################################################################
+sub timestamp {
+	my @months = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
+    my @weekDays = qw(Sun Mon Tue Wed Thu Fri Sat Sun);
+    my ($second, $minute, $hour, $dayOfMonth, $month, $yearOffset, $dayOfWeek, $dayOfYear, $daylightSavings) = localtime();
+    my $year = 1900 + $yearOffset;
+    my $theTime = "$hour:$minute:$second, $weekDays[$dayOfWeek] $months[$month] $dayOfMonth, $year";
+    print "Time now: " . $theTime."\n";
+}