PetGui tutorial

Starting PetGui
Using PetGui
Pipeline editor
- Exporting pipelines
Running programs
Settings

Starting PetGui

To start PetGui graphically, simply doubleclick on its icon. You can also drag saved PetGui sessions and applications onto it to open them. When starting PetGui from the command line, a session or application definition file can be specified as a parameter. Special parameter --help lists all arguments. --pipeline starts PetGui directly in pipeline editor mode.

When started without parameters, PetGui will display the following dialog:

The path on the top is where PetGui searches for application definition files. You can change it by clicking on the Change... button, which opens the settings dialog.

Below is a list of applications found in the directory. To start one, select it from the list and press the Select button, or simply doubleclick the application name.

You can also load a previously saved session by with the Open session button.

Create pipeline starts PetGui in pipeline editor mode.

Using PetGui

When a PetGui application is started, it shows only the required parameters. (This can be changed from the settings dialog). To show the optional parameters, toggle Show options from Application menu.

The version box at the bottom allows you to choose which version of the program to use. Pressing Start will run the program.

Each PetGui application is slightly different, but they all work the same way. All applications have one or more input files. Clicking on the little folfder and disk buttons will pop up a file selection box. The output file is usually optional, if omitted the filename will be automatically generated from the input file.

Pipeline editor

The pipeline editor allows you to group multiple programs together into a batch file. A PetGui pipeline is a batch of programs that will be run in succession. The output file of each program is automatically assigned as the input file of the next one.

PetGui can assign only one input file per program. If the program you wish to use uses multiple input files, you must choose which one will be assigned by PetGui and set the others manually. To select which one will be used in the pipeline, use Input file menu option in application menu.

Some programs also have multiple output files and again PetGui pipelines can use only one of them. Select which one to use from the Output file menu option.

The list of applications in the pipeline is on the left. They will be run in order. You can change the order with the Move up and Move down buttons. Applications in the pipeline are actually saved sessions. You can add one by clicking on Add from file... or create a new one by clicking Add new... When creating a new application session, remember to save your changes for them to take effect. Removing an application with the Remove button will only remove it from the list and will not delete the file. Doubleclicking on an application will open PetGui in application editor mode.

On the right side you can set pipeline and application settings. Input file is the first file fed to the pipeline and output file is the last one it outputs. If Stop pipeline on error is checked, the pipeline execution will be stopped if an error occurs.

The title text box sets the title of the session. The title doesn't affect anything, it is just there to help distinguish between sessions. Checking the Use application defined input file checkbox will disable automatic input file assignment for this application. Use application defined output file does the same for the output file, though it only has effect on the last application in the list.

Exporting pipelines

Pipelines can be exported as shell scripts. Windows batch files and UNIX bourne shell scripts are supported. To export, select the appropriate format from File->Export menu. To ensure file path correctness, you should only export Windows scripts on Windows and UNIX scripts on UNIX.

Running programs

To run the program while in application mode, press the Start button or Run manually from Application menu. In pipeline mode, start the pipeline by clicking Start from Pipeline menu.

The above screenshot shows a completed pipeline. The grey text lines are PetGui messages about process starting and completion. Exit code 0 means the process finished succesfully. Error messages are coloured red. Black text is from the running applications themselves.

Pressing Stop will stop the running process and pipeline. Save log saves the text into a file. Close will close the window. Note that a running program is not terminated and will continue in the background.

Settings

Application path
Where to look for application definition files. Under Windows, this is usually P:\bin\petgui and under UNIX /data/petsoftware/bin/petgui.

Program binary path
Location of the actual programs. Under Windows, this is usually P:\bin\windows and under UNIX /data/petsoftware/bin/intel_unix.

Hide optional parameters by default
If checked, optional parameters will be hidden when an application is loaded.

Change history

11.05.2005 Created by Calle Laakkonen
29.11.2005 Revised by Jarkko Johansson