Center for Computational Genomics and Data Science Manual

The Manual of Operations (MOO) for the Center of Computational Genomics and Data Science provides guidance to members of the center its mission and operations. The manual of operations is a statically generated website using MkDocs which creates a static website from MarkDown files. The following website https://www.markdownguide.org/basic-syntax/ is a useful guide and cheatsheet to MarkDown syntax for formatting.

Local Development with Docker

Docal Pre-requesites

• Docker

Deploy Locally within Docker

If you do not want to install Python or MkDocs directly onto your system, you can use docker and docker-compose to develop with locally. To start running the self-hosted mkdocs service to live update execute the following.

docker-compose up

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Local Development native on computer

Native Pre-requesites

• MkDocs

Installation

MacOs

Homebrew
brew install mkdocs

Windows

Choclately
choco install mkdocs

Deploy Locally

Use the following command to localy update and view hotloaded changes live.

mkdocs serve

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Add new pages

There are two steps to add new pages to the manual of operations.

1. Create a new MarkDown file within the docs/ directory. MarkDown file names use Kebab Case naming scheme. An example is helpful-uab-information.md.
2. Open the mkdocs.yml file within the root project directory. Add a new line under the nav section within the YAML file with the following format - <Page Name>: <mark-down-file-name.md>. The MkDocs shall order the menu the as thenav section in the mkdocs.yml.

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Production

The following commands can only be executed if MkDocs is directly installed on the machine. However, this will rarely be needed when updating the MOO.

Build Website

mkdocs build

Build and Deploy to Gitlab Pages

Reference the .gitlab-ci.yml file for configuration of Gitlab Pages continuous integration for deploying the mkdocs generated website to Gitlab pages.

mkdocs build -d public