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bin/geoCancerDiagnosticDatasetsRetriever  view on Meta::CPAN

		system ("cpan App::cpanminus");
		print color ("green"), "done\n", color("reset");
		print color ("green"), "Installing $cpan_module....\n", color("reset");
		#now install LWP::Protocol::https module
		system ("cpanm $cpan_module");
		print color ("green"), "done\n", color("reset");
	}
	
	#check 3 - check for the presence of curl/lynx binaries in the $PATH. 
	#if not found, install on an Ubuntu/Ubuntu-based systems. 
	#if system is not Ubuntu, prompt user to install it manually.
	my $check_curl = qx{which curl};
	my $check_lynx = qx{which lynx};
	#check if current system is Ubuntu/or Ubuntu-based
	my $ubuntu = qx{uname -a};
	
	if (!$check_curl) {
			
		if ($ubuntu=~ /.+ubuntu.+/ig) {
			
			print color ("red"), "curl binary was not found: follow onscreen instructions/input your password for its installation...\n\n", color("reset");

bin/geoCancerDiagnosticDatasetsRetriever  view on Meta::CPAN

		my @files = glob("$prog_path/data/$cancer\_cancer_GEO_*.txt");
		my @sorted_files = sort {$b cmp $a} @files;
		$run_dir = "$results_subdir" . "$cancer_type\_GEO-files";
		
		foreach my $file (@sorted_files) {
			
			$restart_input_file = basename($file);
			last;
		}

		#If an old run file was found, prompt the user with choices to make.
		if (-e "$run_dir") {
			
			print color ("red"), "$cancer_type\_GEO-files directory exists...This run was not completed\n", color("reset");
			my $text = "";
			my $ok   = timed_response( sub { 	
			
				print color ("red"), "Do you want to resume an interrupted execution [r], or start a new one [n]? (r/n)\nDefault selection will be [n] after 10 seconds...\n", color("reset"); $text = <STDIN>; 
			
			}, 10);