IPC::Run3 will allow you to capture the output as well as the return code from the program you are running.

Untested late night code ;-) 

use strict;
use warnings;

use IPC::Run3;

my ($in, $out, $err);

my @cmd = qw{blastall -i foo -o bar -p blastx -d baz};

eval {
   run3 \@cmd, \$in, \$out, \$err);
}

if ($@) {
   die "[Error] Command encountered an error in IPC::Run3 [$@]\n";
}

if ($?) {
   die "[Error] Command encountered an error [$?]\n";
}

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From the docs...

run3 throws an exception if the wrapped system call returned -1 or anything went wrong with run3's processing of filehandles. Otherwise it returns true. It leaves $? intact for inspection of exit and wait status.

Note that a true return value from run3 doesn't mean that the command had a successful exit code. Hence you should always check $?.

Updated with Perlbotics and Hue-Bond suggested use of qw{}.

In reply to Re: Capture external program return value by tokpela
in thread Capture external program return value by llancet

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