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Command Line Application Help

This topic provides a basic introduction to using software tools that do not have a graphical user interface (GUI) and instead can only be used at the Windows Command Prompt.



Several of the applications available on this site are command-line only applications. This means that they do not have a graphical user interface (GUI) and, instead, must be run via the Windows Command Prompt. The following discussion is provided to help you run command line applications.

Identifying Command Line Applications

You will know the program is a command line application if you see one of the following behaviors:

  • You run the program shortcut (e.g. Start->Programs->PAST Toolkit->Residue Frequency Summarizer) and a black window appears in the background, while a Program Syntax window appears in the foreground (see Figure 1 in CommandLineHelp.pdf, available below)
  • You navigate to the program's folder in C:\Program Files\ and double click the program executable (e.g. ResidueFrequencySummarizer.exe) and, again, you see a black window in the background and a syntax window in the foreground (see Figure 1 in CommandLineHelp.pdf)
  • You run the program (either by shortcut or double clicking the .Exe) and a black window appears very briefly and then disappears (see Figure 2 in CommandLineHelp.pdf)

Running a Command Line Application

In order to properly run a command line application, you will need to follow these steps.  Note that CommandLineHelp.pdf (available below) also includes screenshots for these steps.

  1. Go to the Windows command prompt.  One option is to choose Run from the Windows Start menu, type cmd, and click OK
  2. Use the "cd" command to change to the folder containing the program you wish to run. You can also use the "dir" command to view the files and folders present.
  3. Run the command line program by typing its name and pressing Enter

Program Switches

When running a command line program, you will typically need to pass some information to the program, e.g. a filename to process or a parameter that specifies a processing option. Windows command line programs typically use the / character (forward slash) for a switch, though sometimes the - character (dash) is used instead. In the example shown in the above figure, the /i switch was used to specify the input file for the program, like this:

ResidueFrequencySummarizer.exe /i:TestSequences.txt

Each command line program available on this site should include a Readme.txt file that explains the switches appropriate for the given program. Alternatively, if you run the program without any switches, or with the /? switch, you should see the program syntax, either in a new window or in the command prompt window (as shown in Figures 1 and 2, above).

Additional Information

You can find numerous web pages that describe the use of the command prompt in Windows. For example, the top hits for googling using the windows command prompt include tutorials at these sites:




All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.



These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov

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