UGENE provides command line interface (CLI). To learn more about UGENE CLI and commands available read main UGENE User Manual.

This chapter describes how you can create a new command using a workflow.

To run a workflow from the command line do the following:

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  <img src="/wiki/download/attachments/2097213/Running Workflow from the Command Line_1.png"/>
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It contains the list of objects that corresponds to the elements of the workflow. For each object the list of parameters is available for which you can assign command line aliases. For example, assign alias in to parameter Input file (of the Read alignment element): 

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And alias out to parameter Output file (of the Write Stockholm element). 

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  <img src="/wiki/download/attachments/2097213/Running Workflow from the Command Line_3.png"/>
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To select ports and slots aliases use the following dialog by the Actions->Configure port and slot aliases main menu item: 

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  <img src="/wiki/download/attachments/2097213/Running Workflow from the Command Line_4.png"/>
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Press the Ok button to save aliases and close the dialog. When you create aliases you can import workflow to element by the Actions->Import workflow to element main menu item.

[path_to_ugene\]ugene --task={schema_name} [--{parameter1}={value1} [--{parameter2}={value2} ...]]

The run information will be saved into the text file. By default it is the working directory.

For example on Windows the command can look as follows:

ugene --task=C:\mySchema --in=C:\COI.aln --out=C:\COI.sto

In this example the path to the directory with the UGENE executable is added to the system PATH variable.