Reading it¶

First, you can just read it. Booooring.

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Running it locally¶

Second, you can clone it to your local computer with:

git clone http://github.com/dib-lab/zaok.git

and run it there. You’ll also need to have Python 3.5 and specific versions of khmer and some other software installed – we suggest you create a virtualenv and install those software packages like so:

cd ./zaok/
python3.5 -m virtualenv zaok_env
source zaok_env/bin/activate
pip install -r requirements.txt

Then, you can run:

jupyter notebook &

Running it in a binder on mybinder¶

Third, you can take advantage of mybinder and run it there, by clicking:

Building the full documentation yourself¶

The documentation source (reStructuredText + Jupyter Notebooks) is in the GitHub repository is http://github.com/dib-lab/zaok.git

To build it all, you’ll need to install sphinx, as well as the stuff in requirements.txt.

Then run:

make html

and look in _build/html/ for the output.

The GitHub pages site hosted at https://dib-lab.github.io/zen-khmer/ is in the gh-pages/ branch at https://github.com/dib-lab/zen-khmer. (We do it this way to avoid having to switch branches to update the docs.)

Jupyter Notebook quickstart¶

Shift-ENTER will execute a cell.

You can go in and edit a cell and re-run it with Shift-ENTER.

The Kernel menu has an entry ‘Restart & Run all’, too.