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Running Your Pipeline
Running Within the GUI
The run button is used to start running the commands you added you your pipeline. The output you would normally see on the screen when running mothur from the command line will appear in the Mothur's output box.
You may decide while running your pipeline that you want to pause and make some changes. You can do so with the stop button.
You can restart the running of mothur with the start button.
If you have a pipeline and only want to run a portion of it, you may do so with the start here option. Right click on the command button you wish to start at and select start here.
Running from command line
If you want to run your pipeline using mothur's command line version you can easily convert your pipeline to a batchfile with mothur's create batch file button.
Then you can run mothur in Batch mode: