cleaning up pipeline migration to new trim script and STAR

- updated PIPELINE to use STAR instead of RUM
- enabled HTSEQ in PIPELINE
- print version trimReads.py information in log file
- updated documentation for various modules
- updated TRIM to allow users to specify the contaminants file
- fixed printing of command args in log file
- fixed bug in STAR, incorrectly setting input directory
- fixed debugging mode to not seek version info from external apps
- fixed rsync so that the log file isn't squashed with successful rsync
commands