Is there a reason why you are not using CPAN.pm to install your modules?

If you still need to do the installation locally, the following sequence will install the modules as if you typed the commands yourself:

use Cwd;
my $package = 'Tie-File-0.96';

sub run {
  my (@command) = @_;
  print "Running @command";
  system(@command) == 0
    or die "Couldn't run : $!";
};

my $old_dir = getcwd;
run("tar", "xvzf", "$module.tar.gz" );
chdir $module
  or die "Couldn't chdir into '$module': $!";
run($^X,"-w","Makefile.PL");
run("make");
run("make","test");
run("make","install");
chdir $old_dir
  or die "Couldn't chdir into '$old_dir': $!";
[download]

Update: Added restoral of the old directory

Just to elaborate on the above suggestion, using CPAN.pm would make this trivial. Here's an example:

use CPAN;
use CPAN::Shell;

for(qw/Tie::File Foo Bar/)
{
  CPAN::Shell->install( $_ );
}
[download]

When you code the script, you can have it change to the directory where the makefile.pl is located for all modules to be installed. Something like the following:

chdir "/root/shashi/msa-prereq/Tie-File-0.96/" or die "cannot chdir to
+ /root/shashi/msa-prereq/Tie-File-0.96/: $!";
system "Makefile.pl";
#other code
#other code 
chdir ""/root/shashi/msa-prereq" or die "Cannot chdir to "/root/shashi
+/msa-prereq: $!";
[download]

Repeat the same code for all modules that need installed.

Edit:Updated to change back to /root/shashi/msa-prereq befor changing to the next module folder