Sepsis-Omics Tutorials

Tutorials on how to use the microGVL to do common bacterial bioinformatic tasks.

Deployment

The tutorials have been deployed here: http://sepsis-omics.github.io/tutorials/

How to work on them locally

Install the mkdocs tools

% pip install mkdocs markdown-include mkdocs-alabaster mkdocs-bootstrap

Clone the repo

% git clone https://github.com/sepsis-omics/tutorials.git sepsis-tutorials
% cd sepsis-tutorials

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     # some pages
dna/ prot/ rna/ met/  # some folders with more pages
media/                # folder for 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/dna/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/dna/denovo/minia.md
git commit -m "Added minia" mkdocs.yml docs/dna/denovo/minia.md
git push

Your private local web version http://127.0.0.1:8000/ will also 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 http://sepsis-omics.github.io/tutorials/

Authors

• Torsten Seemann
• Anna Syme
• Simon Gladman
• Dieter Bulach