How do I execute a unix command containing a perl variable in perl - perl

Question

In the following perl code, I am tring to copy a perl variable $file from one directory to another directory with:
"system("cp $file $Output_Dir);
This command writes down the file name alright but then says:
cp: cannot stat 'tasmax_AFR-44_CNRM-CERFACS-CNRM-CM5_historical_r1i1p1_CLMcom-CCLM4-8-17_v1_day_19910101-19951231.nc': No such file or directory
The command
system("#sixfiles = ls $Vars[$kk]}*");
gives me the error:
sh: 1: =: not found
I wonder what is wrong with this code. Assistance will be appreciated.
#!/usr/bin/perl -w
use strict;
use warnings;
use File::Path;
use File::Copy;
my $debug = 1;
my #Vars = ("pr","tasmin","tasmax");
my $Vars;
my #sixfiles;
my $sixfiles;
my $Input_Dir = "/home/zmumba/DATA/Input_Dir";
my $Output_Dir = "/home/zmumba/DATA/Output_Dir";
for (my $kk=0; $kk < #Vars; ++$kk) {
opendir my $in_dir, $Input_Dir or die "opendir failed on $Input_Dir: $! ($^E)";
while (my $file=readdir $in_dir) {
next unless $file =~ /^$Vars[$kk]/;
next if -d $file;
print "$file\n";
print "Copying $file\n" if $debug;
my $cmd01 = "cp $file $Output_Dir";
print "Doing system ($cmd01)\n" if $debug;
system ($cmd01);
system("#sixfiles = ls $Vars[$kk]}*");
}
}

Answer 1

Try this:
use feature qw(say);
use strict;
use warnings;
use File::Spec;
my #Vars = ("pr","tasmin","tasmax");
my $Input_Dir = "/home/zmumba/DATA/Input_Dir";
my $Output_Dir = "/home/zmumba/DATA/Output_Dir";
opendir my $in_dir, $Input_Dir or die "opendir failed on $Input_Dir: $! ($^E)";
while (my $file=readdir $in_dir) {
next if ($file eq '.') || ($file eq '..');
next if -d $file;
next if !grep { $file =~ /^$_/ } #Vars;
say "Copying $file";
$file = File::Spec->catfile( $Input_Dir, $file );
system "cp", $file, $Output_Dir;
}

Answer 2

system ($cmd01);
Gives:
cp: cannot stat '<long-but-correct-file-name>': No such file or directory
This is almost certainly because you are not running the code from $Input_Dir, so that file doesn't exist in your current directory. You need to either chdir to the correct directory or add the directory path to the front of the file name variable.
system("#sixfiles = ls $Vars[$kk]}*");
This code makes no sense. The code passed to system() needs to be Unix shell code. That's the ls $Vars[$kk]}* bit (but I'm not sure where that } comes from). You can't populate a Perl array inside a shell command. You would need to capture the value returned from the ls command and then parse it somehow to separate it into a list.

Answer 3

You can give a try with the following code:
#!/usr/bin/env perl
use strict;
use warnings;
my $debug = 1;
my #Vars = ("pr", "tasmin", "tasmax");
my $Vars;
my $Input_Dir = "/home/zmumba/DATA/Input_Dir";
my $Output_Dir = "/home/zmumba/DATA/Output_Dir";
my $cpsrc, $cpdest = '';
print "No Write Permission: $!" unless(-w $Output_Dir);
for my $findex (0 .. $#Vars) {
$cpsrc = qq($Input_Dir/$Vars[$findex]);
print "$Vars[$findex]\n";
print "Copying $Vars[$findex]\n" if $debug;
my $cmd01 = "cp $cpsrc $Output_Dir";
print "Doing system ($cmd01)\n" if $debug;
system($cmd01);
}
You don't have to go through each file in source dir. You already know the files to copy from source.