Deren Eaton

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Institutional home page

https://eaton-lab.github.io[1]

Arrival and Departure

Tuesday July 25 - Sunday July 30

Lecture Materials

The lecture slideshow is available on-line here: [2](https://eaton-lab.github.io/slides/MBL/). Feel free to follow along on your own. There are some links in the slides that you may be interested in clicking on to see further resources.

Demo and Tutorials

Documentation


The full ipyrad documentation is available here: [3](http://ipyrad.readthedocs.io). We will reference this documentation throughout the workshop and you will want to have it open in a webpage to follow along.

Part I:

During the lecture we will walk-through most of the on-line tutorial and then as a group complete the first introductory tutorial together, and take a close look at the files that are created at each step of the assembly. The first tutorial for the command-line ipyrad tool is here: [4](http://ipyrad.readthedocs.io/tutorial_intro_cli.html).

Part II: We will then explore the alternative way to run ipyrad which is through its Python API. I will show you how to run an interactive Python session as a Jupyter-notebook and to run ipyrad interactively. This will include the following steps, discussed in the slideshow.

1. starting a jupyter notebook

2. ssh connecting to a notebook on a cluster

3. using jupyter

4. running the ipyrad API

5. running the ipyrad analysis tools

6. empirical examples

You can view the notebook here: [5](http://nbviewer.jupyter.org/github/dereneaton/ipyrad/blob/master/tests/cookbook-empirical-API-1-pedicularis.ipynb)

You can download the notebook onto the cluster with this command


wget https://raw.githubusercontent.com/dereneaton/ipyrad/master/tests/cookbook-empirical-API-1-pedicularis.ipynb

References