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: $!";