How to run a Jupyter notebook from a notebook with a different kernel? [duplicate]

Question

I'm trying to run a Jupyter notebook (R) from within a notebook (Python). Using the command:

%run "DESeq2 Analysis.ipynb"

Calls the Noteook and runs it, but gives a Python error. The notebook that is being called (DESeq2 Analysis.ipynb) should be run with the R kernel. DESeq2 Analysis.ipynb runs fine with the R kernel when I run it independently. What appears to be happening is the calling notebook running with a Python 3 kernel is calling DESeq2 Analysis.ipynb and trying to run the code with the Python 3 kernel instead of R kernel.

Is there a way to specify the kernel when using the %run command?

Answer 1

From @Louise Davies answer to Can Jupyter run a separate R notebook from within a Python notebook?

I don't think you can use the %run magic command that way as it executes the file in the current kernel.

Nbconvert has an execution API that allows you to execute notebooks. So you could create a shell script that executes all your notebooks like so:

#!/bin/bash
jupyter nbconvert --to notebook --execute 1_py3.ipynb
jupyter nbconvert --to notebook --execute 2_py3.ipynb
jupyter nbconvert --to notebook --execute 3_py3.ipynb
jupyter nbconvert --to notebook --execute 4_R.ipynb

Since your notebooks require no shared state this should be fine. Alternatively, if you really wanna do it in a notebook, you use the execute Python API to call nbconvert from your notebook.

import nbformat
from nbconvert.preprocessors import ExecutePreprocessor

with open("1_py3.ipynb") as f1, open("2_py3.ipynb") as f2, open("3_py3.ipynb") as f3, open("4_R.ipynb") as f4:
    nb1 = nbformat.read(f1, as_version=4)
    nb2 = nbformat.read(f2, as_version=4)
    nb3 = nbformat.read(f3, as_version=4)
    nb4 = nbformat.read(f4, as_version=4)

ep_python = ExecutePreprocessor(timeout=600, kernel_name='python3')
#Use jupyter kernelspec list to find out what the kernel is called on your system
ep_R = ExecutePreprocessor(timeout=600, kernel_name='ir')

# path specifies which folder to execute the notebooks in, so set it to the one that you need so your file path references are correct
ep_python.preprocess(nb1, {'metadata': {'path': 'notebooks/'}})
ep_python.preprocess(nb2, {'metadata': {'path': 'notebooks/'}})
ep_python.preprocess(nb3, {'metadata': {'path': 'notebooks/'}})
ep_R.preprocess(nb4, {'metadata': {'path': 'notebooks/'}})

with open("1_py3.ipynb", "wt") as f1, open("2_py3.ipynb", "wt") as f2, open("3_py3.ipynb", "wt") as f3, open("4_R.ipynb", "wt") as f4:
    nbformat.write(nb1, f1)
    nbformat.write(nb2, f2)
    nbformat.write(nb3, f3)
    nbformat.write(nb4, f4)

Note that this is pretty much just the example copied from the nbconvert execute API docs: link