Tutorials on how to use the microGVL to do common bacterial bioinformatic tasks.
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
% 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
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
- Torsten Seemann
- Anna Syme
- Simon Gladman
- Dieter Bulach
- Dominique Gorse
- Xin-Yi Chua
- Mike Thang