Fix issues with calling APAtrap perl scripts

Bug fixes

1. Explicitly call APAtrap perl scripts using the version of perl in the environment, rather than the version of perl referenced in the shebang line of the perl scripts themselves
2. Fix miRanda wildcard recursion issue
3. Add missing 'temp' tags within the 'get_utr_and_cds' module Snakefiles
4. Alter the species config files to in order to remove chromosomes without annotated 3'UTR sequences, which leads to errors