This maybe an OS issue - I’m working with Ubuntu on Windows. Everything is fine - e.g. the gwas analysis runs. However, I need to bypass the code line:


Otherwise I get issues: First, the prompt changes to “In :” and from here when I enter:


I get the error: NameError: name ‘hl’ is not defined

If I run without hl.plot.output_notebook() everything is fine but the plots don’t show (however, the analyses run without any error). Moreover, trying to save the plots with bokeh seems to have the same dependency problems.

I assume this is an IPython issue: I ran pip install IPython but didn’t solve.

You’re running in IPython, not Jupyter, right?

In that case, just remove all the plotting stuff. I have no idea what hl.plot.output_notebook (which is an alias for bokeh.io.output_notebook does when javascript is not available!