Welcome on the training Microbial Comparative Genomics github repository of the Southgreen Bioinformatics Platform

The course itself lives https://southgreenplatform.github.io/training_bacterial_comparative_genomics/, where you can find all the relevant information.

For collaborators teachers and developers

This part is for collaborators-teachers and developers.

Modify content

When you are in the repository, add and/or modify your markdown tutorials in the docs directory. The arborescence of the website menu is to setup in the mkdocs.yml file

Mkdocs

To generate the static web site.

Welcome to MkDocs

For full documentation visit mkdocs.org.
For full documentation about the material mkdocs theme.

Installation

Manual

As prerequisite you need python >=3.8 and pip.

Install Mkdocs:

pip install mkdocs

For the theme:
pip install mkdocs-material

For the extensions:
pip install pymdown-extensions

For the plugins:
pip install mkdocs-minify-plugin
pip install mkdocs-macros-plugin

Conda

Clone the repository and move in it.
Then install all dependencies using conda and the conda_env.yml shipped with this repo:

conda env create -f conda_env.yml

Activate the environment and you are good:

conda activate education

Testing and building the website

• mkdocs serve - Start the live-reloading docs server, to test the site locally (http://127.0.0.1:8000/).

• mkdocs gh-deploy - Deploys the site on github pages.

• mkdocs build - Build the documentation site.

• mkdocs new [dir-name] - Create a new project.

• mkdocs -h - Print help message and exit.

Thanks

Thanks to i-Trop IRD platform for support on docker VM creation and data storage.

Special thanks to IFB for support and availability of VM on Biosphere !