$genes = $ARGV[3];
$isoforms = $ARGV[4];
$trans = $ARGV[0];
$left = $ARGV[1];
$right = $ARGV[2];

$directory = "/home/applications/galaxy-dist/tools/VELVET-OASES";

$transcript = "$directory/trans.fa";
$left_read = "$directory/left_read.fastq";
$right_read = "$directory/right_read.fastq";

symlink $trans, $transcript;
symlink $left, $left_read;
symlink $right, $right_read;

@out = `perl /home/applications/galaxy-dist/tools/VELVET-OASES/run_rsem.pl 2>&1`;