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https://juke34.github.io/awesome-genome-annotation/
Awesome genome annotation tool list
https://juke34.github.io/awesome-genome-annotation/
Last synced: about 1 month ago
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Awesome genome annotation tool list
- Host: GitHub
- URL: https://juke34.github.io/awesome-genome-annotation/
- Owner: Juke34
- License: cc-by-4.0
- Created: 2024-03-05T14:46:32.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2024-03-06T14:13:41.000Z (9 months ago)
- Last Synced: 2024-08-03T23:12:18.151Z (4 months ago)
- Homepage: https://juke34.github.io/awesome-genome-annotation/
- Size: 637 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- awesome-awesomeness-bioinformatics - Awesome Genome Annotation
README
[![CC BY 4.0][cc-by-shield]][cc-by]
# Awesome genome annotation
---------------------------
A curated list of awesome genome annotation tools.
Available here [https://juke34.github.io/awesome-genome-annotation/](https://juke34.github.io/awesome-genome-annotation/).
Please feel free to [contribute](CONTRIBUTING.md)!
## Table of Contents
* [Foreword](#foreword)
* [Project layout](#project-layout)
* [For collaborators teachers and developers](#for-collaborators-teachers-and-developers)
* [Modify content](#modify-content)
* [MkDocs](#mkdocs)
* [Welcome to MkDocs](#welcome-to-mkdocs)
* [Installation](#installation)
* [Manual](#manual)
* [Conda](#conda)
* [Testing and building the website](#testing-and-building-the-website)
## Foreword
You can find here the list of genome annotation tools I have gathered during my bioinformatician life.
The data are located into docs/ and the static website made from this repo lives [https://juke34.github.io/awesome-genome-annotation/](https://juke34.github.io/awesome-genome-annotation/).
## Project layout
```
README.md # General readme
mkdocs.yml # The configuration file for the site rendering.
conda_env.yml # Conda env to build and test the site locally
docs/ # material that will be publish with the static web site
Readme.md # The documentation homepage (Website Home page).
pages/ # Folder dedicated to a topic
images/ # Folder containing images related to the topic
xxx/ # Folder containing the .md files related to the topic topic
...
Images # Images used in the README
```
## 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
#### Welcome to MkDocs
For full documentation visit [mkdocs.org](https://www.mkdocs.org).
For full documentation about the [material mkdocs theme](https://squidfunk.github.io/mkdocs-material/).
#### 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`
`pip install mkdocs-embed-external-markdown`
##### 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.
[cc-by]: http://creativecommons.org/licenses/by/4.0/
[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg