Hardklör is run from a command line. For simplicity, only a single argument is required, the name of the configuration file. Details for setting your configuration file and the parameters contained within can be found from their respective links. The recommended way to operate Hardklör is to store the data and configuration file in a convenient directory, navigate to it, then execute the Hardklör application with the configuration file:
$ cd projects/data_set1
$ /usr/bin/hardklor data_set1.conf
In the above example, you would substitute your own data directories, configuration file, and path to Hardklör with the appropriate names and locations for your installation.
Microsoft Windows users may have difficulty finding their command line prompt. It can be quickly accessed from the Start Menu by typing "cmd" in the menu search box. Once open, it operates similarly to a Unix/Linux prompt (or perhaps more accurately, a DOS prompt).
The first statement you should see printed to the screen is the version, date, and source information for Hardklör:
Hardklör v2.21, July 27 2015
Mike Hoopmann, Mike MacCoss
Copyright 2007-2015
University of Washington
This information is important as Hardklör is in continuous development and different versions may produce different results. It is recommended that you use the latest version of Hardklör, but it may be helpful to also maintain legacy versions so that results may be replicated at a later date.
Analysis progress is reported during execution. The following stages are reported to the user:
Spectral analysis is the core stage of execution where isotopic features are identified. The total analysis time is reported last and the command prompt is returned to the user.
After completion of the algorithm, results will be exported to the storage device. Unless otherwise specified in the configuration file, exported files will be in the current working directory that you navigated to prior to starting Hardklör. All exported results are in text format. Additional details describing these results can be found on the blank page.