Dear Monks,
I have written a PERL script to automate some repetitive Linux (BASH) commands (I suppose I could have written a shell script but I have had little experience doing that). What it is supposed to do is read in every file in a directory rename each file and then execute it (using a program called MODELLER). I am aware that lots of file overwriting is going to take place and am fine about this (I have used cp -f to force copying). Unfortunately no copying is taking place in the specified directory (or anywhere else that I can see) can anyone suggest why? 
do {
opendir(DIR, $dirname) or die "can't opendir $dirname: $!";
while (defined($file = readdir(DIR)))     {
system("/bin/cp -f $dirname/$file malign.top");
system("/bin/cp -f $dirname/$file get-model.top");
system("/usr/local/modeller6v2/bin/mod6v2 $dirname/malign.top");
system("/usr/local/modeller6v2/bin/mod6v2 $dirname/get-model.top");
$m++;
}
} until ($m==2);   #want the whole process to occur twice             
+   
closedir(DIR);

exit;

[download]
Humbly submitted

In reply to automating linux commands in perl by Anonymous Monk

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