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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=0.0.0.0 2>&1 | sed s/0.0.0.0/$(curl -s ipinfo.io/ip)/g
[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 <http://129.114.104.169:8888/?token=483a27cd0387ccd04133570999ba8ce8072cf0f45663289f>`__
[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 <http://129.114.104.169:8888/?token=483a27cd0387ccd04133570999ba8ce8072cf0f45663289f>`__ ## Copy and paste this link in the browser

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

WQ-Maker15

Here is the example Jupyter notebook that was ran before

Jupyter Example

Note

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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