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pipeline.html contains the following sentence

Don’t run the pipeline directly from $JOSHUA. We recommend creating a run directory somewhere else to contain all of your experiments in some other location. The advantage to this (apart from not clobbering part of the Joshua install) is that Joshua provides support scripts for visualizing the results of a series of experiments that only work if you

This is incomplete and needs to be augmented in order for it to make sense.

Make sure to add updating Homebrew.