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MAKER Genome Annotation using cc-tools and Jetstream(WQ-MAKER)

Part 4: Set up a MAKER run using the Jupyter notebook

Step1: Running “tmux” command to run the anlaysis in the background:

$ cd ~
$ tmux

Step2: Copy the example Jupyter notebook onto your home directory:

$ cp /opt/WQ-MAKER_example_data/WQ-MAKER-Jupyter-notebook.ipynb .

Step3: Launch jupyter notebook in the background:

$ python /opt/anaconda2/bin/jupyter-notebook --no-browser --ip= 2>&1 | sed s/$(curl -s
[I 16:54:10.440 NotebookApp] Writing notebook server cookie secret to /run/user/1000/jupyter/notebook_cookie_secret
[I 16:54:10.650 NotebookApp] Serving notebooks from local directory: /home/upendra
[I 16:54:10.650 NotebookApp] 0 active kernels
[I 16:54:10.650 NotebookApp] The Jupyter Notebook is running at:`Jupyternotebookrunninglink <>`__
[I 16:54:10.650 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 16:54:10.650 NotebookApp]

    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        `Copylinkbelow <>`__ ## Copy and paste this link in the browser

Step 4: Now click open “WQ-MAKER-Jupyter-notebook.ipynb” and run the jupyter notebooks.


Here is the example Jupyter notebook that was ran before

Jupyter Example


If you want to exit out of tmux shell without killing it. Press ctrl + b and d. If you want to kill it. Then press ctrl +c

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