McGill SI 2018

Tutorials for microbial genomics and genomic epidemiology.

Deployment

The tutorials have been deployed here: https://sepsis-omics.github.io/mcgill-si-2018/

How to work on them locally

Install the mkdocs tools

% pip install --upgrade mkdocs markdown-include mkdocs-extensions mkdocs-material

Clone the repo

% git clone https://github.com/sepsis-omics/mcgill-si-2018.git
% cd mcgill-si-2018

Browse the site locally without deploying to public internet

% mkdocs serve

Open your web browser to http://127.0.0.1:8000/ and leave it open. This will update automatically as you make changes to the documenation.

The master document is a YAML file

% less mkdocs.yml

The actual Markdown pages are in the docs folder:

% ls docs
index.md about.md modules/ 

# modules/lessons
% cd modules
% ls

dna/ prot/ rna/ met/  

# the content for a module
% cd dna
% ls dna
index.md images/

To add a new page, say a page on the 'Minia' genome assembler, find the right location and create a page. In this case it would be docs/modules/denovo/minia.md. Write the tutorial in that file, and then add the file to the master document mkdocs.yml in the correct section.

When you are happy, add it the repo

git add docs/modules/denovo/minia.md
git commit -m "Added minia" mkdocs.yml docs/modules/denovo/minia.md
git push

Your private local web version http://127.0.0.1:8000/ will also auto-update.

To deploy the whole lot to the public website

mkdocs gh-deploy --clean --message "Added minia"

This first builds a web HTML version of our Markdown hierarchy into the site/ folder, then pushes it to a special branch of the github repo called gh-pages which GitHub makes available at the public URL https://sepsis-omics.github.io/mcgill-si-2018/

Authors

• Anna Syme
• Torsten Seemann
• Simon Gladman
• Dieter Bulach
• Anders Goncalves da Silva
• Lauren Cowley