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.