Materials and data for the Penn State Data Analysis Bootcamp

The bootcamp is about reproducible research. Let's see if we can reproduce the site that is about reproducible research... Hmmm...

How to generate the site

First of all note that you don't actually need to fully generate this site yourself during the bootcamp. These instructions are here just to explain the process. But even if you don't generate the site itself you may still contribute to it via the GitHub web interface or after cloning locally.

The website is generated from the files in the web directory of the bootcamp-central repository via the pyblue python package. For it work you would need to have both Python and the pip package manager installed.

Clone the repository:

git clone https://github.com/biostars/bootcamp-central

Install pyblue of a specific version. It is best if you use a virtual environment, for example conda.

conda create --name bootcamp python=3 -y

activate the new environment:

conda activate bootcamp

Install pyblue of a version that is known to accept the markup we use:

pip install pyblue --upgrade

You can now view the site as HTML with:

cd bootcamp-central

the default Makefile action is to run the server:

make

or

pyblue -r web

This will start a web server on your computer and you can use the browser to view the contents of the site. This is used while developing the site.

http://localhost:8000

To generate a published version of the site add the -o parameter with a directory name that is meant to store the output destination

pyblue -r web -o /final/directory