routine can now be run as part of a cycle so that analysis finishes directly instead of post-processing

original run scripts now in the example dir. Copies should go to the da/trunk/ main dir before running

original run scripts now in the example dir. Copies should go to the da/trunk/ main dir before running

original run scripts now in the example dir. Copies should go to the da/trunk/ main dir before running

Changed the template for submitting a new job when in interactive or background mode. The output is now directly piped to the log file instead of first collected and then moved at the very end of the step. Reason is because it was difficult to manage the output from stdout since we have a shell script executing a python command, and resubmitting through a new shell script. Thsi was impossible to a=capture in separate output files unless the name of the pipe was specifically added to the shell script command line. Note that all job files now end up correctly, except for the first one which is piped to screen or to a specified file.