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---
title: "Tutorial for Github and R markdown"
subtitle: "HUST Bioinformatics course series"
author: "Wei-Hua Chen (CC BY-NC 4.0)"
institute: "HUST, China"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
beamer_presentation:
theme: AnnArbor
colortheme: beaver
fonttheme: structurebold
highlight: tango
includes:
in_header: mystyle.sty
---
```{r include=FALSE}
color_block = function(color) {
function(x, options) sprintf('\\color{%s}\\begin{verbatim}%s\\end{verbatim}',
color, x)
}
## 将错误信息用红色字体显示
knitr::knit_hooks$set(error = color_block('red'))
```
## TOC
1. install Github, sign up and sign in
2. clone existing repository (e.g. this repo) to local computer, and get updates
3. create a new repository, add contents and upload to Github server
4. R markdown
## what is Github?
* GitHub是一个面向开源及私有软件项目的托管平台
* 支持git 作为唯一的版本库格式进行托管
* GitHub于2008年4月10日正式上线
* 2018年6月4日，被微软75亿美元收购
**注**：资料来自百度百科
# 1. install Github, sign up and sign in
## 下载 Github desktop
go to: desktop.github.com
{height=60%}
## the welcome screen
start the app, and choose sign up (or sign in if you have an account)
{height=60%}
## sign up
click the sign up link, you will be redirected to the Github website in a browser
{height=60%}
## sign in
create a new account, go back to the desktop app to sign in
{height=60%}
# clone a existing repository and update
## clone a repository, step 1
From your Github desktop app
{height=60%}
## clone a repository, step 2
repository: ```evolgeniusteam/R-for-bioinformatics ```
{height=60%}
## clone a repository, step 3
{height=60%}
## clone a repository, step 4
{height=60%}
## check the local folder
go the local github folder, and check the files downloaded from Github
{height=60%}
## pull updates, step 1
**pull**: 是从repository下载project或更新的过程
点击 "Fetch origin"按钮，如果有更新，它会变为：“Pull origin”:
{height=60%}
## pull updates, step 2
完成更新后，可通过"History" tab 查看更新内容
{height=60%}
**注**：定期检查更新，以获取最新内容
# 3. create a new repository and push to Github
## create a new repo on your computer
from the Github desktop app, select "File" menu -> "New depository ... "
{height=30%}
## create a new repo, step 2
{height=60%}
## create a new repo, step 3
{height=40%}
## open the repo using Atom
Atom can be downloaded from: https://atom.io
){height=50%}
## view and edit repo using Atom
{height=50%}
Please read more about markdown at here: https://guides.github.com/features/mastering-markdown/
## edit and preview markdown file
enable the "Markdown Preview Enhanced" package to preview the markdown file on the fly. This package should be obtained from: https://atom.io/packages/markdown-preview-enhanced.
{height=50%}
## go back to Github desktop app
changes will be highlighted in the Github desktop app
{height=50%}
## publish the newly created repository
{height=50%}
## check the new repository at Githup website
the url will be : <your_username>/<your_repo_name>
{height=50%}
## upload newly added contents and/or changes to Github website
first, use the Github desktop app to upload (push) new contents and/or changes
{height=60%}
## upload newly added contents and/or changes to Github website, cont.
then use the "Push origin" button to actually upload the changes
{height=60%}
## Atom also 'knows'
Atom then 'knows' that the changes have been synchronized to Github:
{height=60%}
# 使用R markdown
## to be continued ...