"if -clean is specified, all files except for those listed in the variables INPUTS\n" "and OUTPUTS get removed from the current directory\n"
"if -clean is specified, all files listed in the TEMPS var get removed\n"
void printHelpText(){  cout <<     "\n"    "USAGE:\n"    "\n"    "runAmos -C config_file [-D VAR=value] [-s start] [-e end] [-clean] [-ocd] prefix\n"    "\n"    "if the config file is not specified we use environment variable AMOSCONF\n"    "if a start step is specified (-s) starts with that command\n"    "if an end step is specified (-e) ends with the command prior to the number\n"    "if -clean is specified, all files except for those listed in the variables INPUTS\n"    "and OUTPUTS get removed from the current directory\n"    "if -ocd is specified checks that all files in the INPUTS variable exist\n"    "\n"    "e.g.  runAmos -s 1 -e 5   will run steps 1, 2, 3, and 4.\n"        "Special variable PREFIX gets set to the prefix specified in the command line\n"    "Lines starting with # are comments\n"    "Lines starting with ## get displayed when next command is run\n"    "\n"    "Example config file:\n"    "\n"    "PATH = /usr/local/bin  # can also be set with -D command line option\n"    "PERL = $(PATH)/perl\n"    "\n"    "1: $(PERL) $(PREFIX).pl\n"    "2:\n"    "$(PERL) $(PREFIX)-1.pl\n"    "$(PERL) $(PREFIX)-2.pl\n"       << endl;} // printHelpText