---
title: "Lab 1: SSH, Keys, R/RStudio, and git clone on MacOS"
author: "Hua Zhou"
date: "Jan 6, 2022"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

This tutorial is for Mac users. For Windows users, please first read the [tutorial](https://ucla-biostat-203b.github.io/2022winter/labs/lab01/lab01_windows.html) to install `Git for Windows`, which ships with `Git Bash`, then most bash commands in this tutorial will work in `Git Bash`.

# Connect from your Mac to teaching server

1. SSH client on MacOS. 
    - MacOS: open the `Terminal` app. You can find `Terminal` from `LaunchPad` -> `Other`, or from `Spotlight Search` (type Terminal). For convenience, you can pin the Terminal program to the Dock.   
    - Check that current shell is Bash   
    ```{bash, eval=F}
    echo $SHELL
    ```
    - If necessary, change default shell to Bash by following command in Terminal. Then close the Terminal window and reopen it.
    ```{bash, eval=F}
    chsh -s /bin/bash
    ```
    
    
2. Connect to the teaching server. On MacOS Terminal:  
    ```{bash, eval=F}
    ssh [USERNAME]@server.ucla-biostat-203b.com
    ```
Replace `[USERNAME]` in the command by your actual user name (your email name in MyUCLA). If you cannot connect, you may not have an account. Ask TA or instructor for help.

3. Change password on teaching server
    ```{bash, eval=F}
    passwd
    ```

4. You can use git to obtain a copy of course materials:
    ```{bash, eval=F}
    git clone https://github.com/ucla-biostat-203b/2022winter.git
    ```

# Install R and RStudio on your own machine. 

1. Install R v4.1.2 or later. <https://cran.rstudio.com>

2. Install RStudio Desktop (Open Source Edition). <https://rstudio.com/products/rstudio/#Desktop> 

# Git

Check whether `git` command is available in Terminal. If not, follow instructions at <https://git-scm.com/book/en/v2/Getting-Started-Installing-Git> `Installing on macOS` section to install it.

# `git clone` and `git pull` course materials

1. On whichever machine that has `git` installed, e.g., your Mac Terminal or teaching server, you can obtain the 203B course material by command
```{bash, eval=F}
git clone https://github.com/ucla-biostat-203b/2022winter.git [<dir>]
```
Replace `[<dir>]` by your preferred folder name, say `203b-2022winter`. 

2. The Git repository <https://github.com/ucla-biostat-203b/2022winter.git> is frequently updated. To sync your git clone with the current repo., first enter your local repo directory
```{bash, eval=F}
cd /PATH/TO/LOCAL/REPO
```
then 
```{bash, eval=F}
git pull
```
If you have made commits to the local repo, then the two commits need to be merged. 

3. Besides command line, we can also use **RStudio** to perform git clone and many other git operations. To git clone a repository, in RStudio `File` -> `New Project...` -> `Version Control` -> `Git`, then copy the **git address** (not **HTTPS** address) `git@github.com:ucla-biostat-203b/2022winter.git` to the `Repository URL:`. 

# Access RStudio on the teaching server

Open your browser and enter address <http://server.ucla-biostat-203b.com:8787> to use RStudio **on the teaching server**. Log in using your credential for the teaching server. 

# SSH keys

1. First check whether you already have keys on your local machine.
```{bash, eval=F}
ls -al ~/.ssh
```
If you don't have `~/.ssh` folder, that means you have never used SSH before.

2. If no SSH keys yet, generate a pair of SSH RSA keys
    - Method 1: generate keys on MacOS Terminal or Windows Git Bash. Follow [instructions in lecture notes](https://ucla-biostat-203b.github.io/2022winter/slides/02-linux/linux.html#steps-to-generate-keys).  
    - Method 2: Use RStudio to generate keys. `Tools` -> `Global Options...` -> `Git/SVN`. 
Using either method, make sure keys are in the default location `~/.ssh/`

3. Make sure the permission for the key files are correct.   
    - On MacOS terminal: 
        - The permission for the `~/.ssh` folder should be `700 (drwx------)`. 
        - The permission for the private key `~/.ssh/id_rsa` should be `600 (-rw-------)`. 
        - The permission of the public key `~/.ssh/id_rsa.pub` should be `644 (-rw-r--r--)`.
    - On Window Git Bash, the following permission could also work: 
        - The permission for the `~/.ssh` folder can be `755 (drwxr-xr-x)`. 
        - The permission for the private key `~/.ssh/id_rsa` can be `644 (-rw-r--r--)`. 
        - The permission of the public key `~/.ssh/id_rsa.pub` can be `644 (-rw-r--r--)`.
    
4. On the teaching server, put the same pair of keys under `~/.ssh`. 
    - The permission for the `~/.ssh` folder should be `700 (drwx------)`. 
    - The permission for the private key `~/.ssh/id_rsa` should be `600 (-rw-------)`.
    - The permission of the public key `~/.ssh/id_rsa.pub` should be `644 (-rw-r--r--)`. 
    - The `authorized_keys` file should contain the public key (cannot duplicate) and its permission should be `600 (-rw-------)`.

5. Now try to SSH into the teaching server from your Mac. If keys are set up correctly, you should be able to connect to the teaching server **without entering password**.
```{bash, eval=F}
ssh [USERNAME]@server.ucla-biostat-203b.com
```