#!/usr/bin/perl

use File::Temp qw/ tempfile tempdir /;
use File::Copy qw/ copy /;
use Cwd;

$mirna_file = $ARGV[0];
$trans_file = $ARGV[1];
$targets = $ARGV[2];

# do all the dirty work in a temp directory
$cwd = cwd();
$tempdir = tempdir(CLEANUP => 1);

copy ("/data/galaxy/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/mirdeep2_and_targetspy/798fe7ba8b5e/mirdeep2_and_targetspy/mirdeep2/target_spy_wrapper.sh", $tempdir);
chdir ($tempdir);

$ret_ts = `sh target_spy_wrapper.sh $mirna_file $trans_file`;
if ($ret_ts ne "") {die "TargetSpy error"}
copy ("targets", $targets);

chdir($cwd);