Table of Contents

• Do You Belong Here?
• An Example Provided
• Starting a New Handout Project
  • Installing Hub
  • Create a New GitHub Repo Based on handout-template
• Adding New Content to Your Handout
  • Using the Supplied Paragraph Text Environments
  • Adding a Table
• Merge in Updates From handout-template
• Credits
• License

Do You Belong Here?

This README.md file contains nitty-gritty details of how to use this repository for developing your own hands-on workshop handout. For example, you shouldn't be scared off by the prospect of trying things like:

• Cloning git repositories
• Adding upstream remotes
• Installing a LaTeX environment for building PDFs from the source LaTeX
• Setting up Travis Continuous Integration (Travis-CI) for automating the PDF build process

The idea is to help you go from the barebones contents of this repository to a fully-fledge LaTeX document like the one developed for an NGS Workshop:

• Trainee Handout PDF
• Trainer Handout PDF

An Example Provided

We have provided a short example example.tex demonstrating the main features. The PDFs built directly from this example can be found here:

• Trainee Example PDF
• Trainer Example PDF

Starting a New Handout Project

There are some established git and GitHub workflows when it comes to cloning a repository. However, we can assume your planned future handout document is going to differ significantly from the way this repository looks right now.

I recommend the following approach:

Installing Hub

To install hub you first need to install rake, a ruby make-like utility. On Ubuntu this can be achieved using apt-get:

# Install rake
sudo apt-get install -y rake

# Clone and install hub
git clone https://github.com/github/hub.git
cd hub
sudo rake install prefix=/usr/local

Wherever we need to use hub, as opposed to git, we'll be explicit in the code which follows.

Create a New GitHub Repo Based on handout-template

my_new_handout_project='my_new_handout'

# Clone the handout-template repo
hub clone --origin template BPA-CSIRO-Workshops/handout-template "${my_new_handout_project}"
cd "${my_new_handout_project}"

# Create a new project on GitHub to house your new handout project
hub create "${my_new_handout_project}"

# If you want to create the repository within an organisation, you can do something like:
# my_organisation='BPA-CSIRO-Workshops'; hub create "${my_organisation}/${my_new_handout_project}"

# Push the code into your newly created repository on GitHub
git push -u origin master

You can now modify the files and push the changes to your new GitHub repo:

git push

Adding New Content to Your Handout

Using the Supplied Paragraph Text Environments

Adding paragraph text to the handout is simple, thanks to the style file provided. You simply place your text within one of the paragraph "environments" to have it styled appropriately. In practice, this means you place a \begin{environment-name} before your paragraph text, and \end{environment-name} after your paragraph text. Here is a table of the environments supplied in the style file in this template:

Environment Name	Purpose
information	For providing background information to the reader.
steps	For providing instructions on the steps the reader is required to take.
note	For providing additional information for future reference.
warning	For providing a warning which should be read before the reader continues.
questions	For posing questions to the reader.
answer	For providing the answer to the preceding question.
bonus	For providing bonus information, exercises and questions to a quickly advancing reader.
advanced	For providing advanced information, exercises and questions to a very quickly advancing reader.
lstlisting	For providing code to the reader.

Adding a Table

Adding a table in LaTeX is somewhat more difficult than adding standard paragraph text. The most straightforward way to accomplish this is by using an online LaTeX table generator.

Merge in Updates From handout-template

The beauty of having the handout-template as an upstream, is that you can easily pull in any changes from that repository:

# Fetch any changes from your own GitHub repository
git fetch origin

# Fetch any changes to the template
git fetch template

# Merge changes into your working directory
git merge template/master

# Push changes back to your own GitHub repository
git push

Credits

This style was originally designed for the Next Generation Sequencing (NGS) hands-on workshop developed by Bioplatforms Australia (BPA), CSIRO Bioinformatics Core and the EBI. It was written predominantly by Nathan S. Watson-Haigh.

License

The contents of this repository are released under the Creative Commons Attribution 3.0 Unported License. For a summary of what this means, please see: http://creativecommons.org/licenses/by/3.0/deed.en_GB