install_samtools.sh: updated to use wrapper functions and make script more concise.
install_samtools.sh: minor improvement for logging output of make steps.
install_MEME.sh: updated to use wrapper functions and make script more concise.
install_freebayes.sh: updated to use wrapper functions and make script more concise.
functions.sh: 'do_make' also reports the arguments.
install_fastx_toolkit.sh: updated to use wrapper functions and make script more concise.
install_BEDTools.sh: updated to use wrapper functions and make script more concise.
functions.sh: add --exe option to copy_files to only copy executables (now also skips non-file items).
install_rsem.sh: updated to use wrapper functions and make script more concise.
install_mothur.sh: use wrapper functions to make script more concise.
build_perl.sh: use wrapper functions to make script more concise.
build_python.py: various updates including using wrapper functions and trapping for ez_setup.py failed.
build_R.sh: updated to use wrapper functions and make script more concise.
functions.sh: update check for empty args in 'do_configure' (previously sometimes gave an error).
functions.sh: new functions 'set_env_var' and 'check_program'.