Shell Command.Rmd

---
title: 'Shell Commands'
author: "Nicholas J. Gotelli"
date: "23 April 2024"
output:
  html_document:
    highlight: tango
    theme: united
  pdf_document: default
---

# PS1='$ '

*Most of the following commands can be completed in Windows Powershell. For important information on `cmd` and Powershell for Windows users, see the [Windows cmd Glossary](WindowsCmdGlossary.html).*

___

### Shell preliminaries
- 1971 earliest unix shell
- interface keyboard and a teletype
- faster than mouse, better than gui for complicated or repeated activities
- dominant until appearance of personal computers
- still dominant for critical systems (NASA,hospitals, military, air traffic control)
- uses plain-text files
- important for -omics pipelines and working with large data
- bash shell (= bourne again shell)

### System problems
- iOS no problem because underlying unix
- Windows problem because Windows powershell is not comparable; use `Cygwin`
- RStudio has limited shell installation for use with git but not much else
- compatability problems and minor differences very common

### Learning how to navigate the shell
- Windows systems use mouse and have eagle eye view
- Shell uses keyboard and has an ants eye view 
- Learning navigation is single most important thing for working with shell
- Always use tab completion for the names of directories and files (will not work on commands, however)

### The organization of a computer
- Hierarchical tree from root to branch tips with forks
- Files and folders versus files and directories
- All files correspond to a directory, but not vice versa
- Keys to the entire factory
- Hard drive or desktop are not the root of your computer
- Be careful on the factory floor

### The `pwd` command
- shell always points to a specific directory
- There is an absolute path to a directory
- Use forward slashes for unix path specification
- Absolute path traces from root of the computer
- Uses forward slashes (in contrast to Windows)
- `/` indicates top level root of entire program
- `pwd` gives /path/to/current/directory

### Open shell
- `$pwd /Users/nickgotelli
- this always tells me where I am

### The `ls` command
- `ls` lists files and lower level directories in current directory
- demonstrate for my system

### Absolute versus relative path statements
- absolute path always starts at root `/Users/nickgotelli/Desktop`
- absolute paths work from anywhere within your system
- relative path does not start with forward slash but with name of directory within your current directory. If I am in my home directory, I can just use `Desktop` or `Desktop/` to indicate this subdirectory, which is relative to my current path

#### Useful options with `ls`
- `ls -a` shows all including hidden files
- `ls -l` long format with lots of detail
- `lf -R` recursively list subdirectories (careful!)
- `ls -1` list one item per line (useful for programming)
- `ls -G` list files and directories in color
- `ls -F` use symbols for different file types
    + no symbol = file
    + `/` = a directory
    + `*` = an executable shell script
    
#### EXERCISE: Open shell, do a listing with ls -GF

### The `cd` command
- use this to move around in different subdirectories
- most basic form `cd <directory name>` only works for directories that are "below" your current directory (subdirectories)

#### EXERCISE: Open shell `ls cd Desktop`
- now try moving to a subdirectory on your desktop, followed by ls

### Key built in short-cuts
- shell opens in your `home` directory
- `cd ~` always returns you to home in one jump
- `cd` also takes you home with one less symbol to type
- `/` takes you to top level root of your computer (rarely needed)
- `cd DirectoryA/SubdirectoryOfA` jumps you down two directories in a single step
- `cd ..` moves you up to the next highest directory
- `cd ../..` jumps you up two directories

#### Exercise:
- move down to a folder in your desk top one step at a time
- at each step, check your location (pwd) and list the files(ls)
- now move back up one step at a time all the way to the root
- now can you get back to your desktop folder in one step? something like `cd Users/nickgotelli/Desktop/Directory`
- now jump to your home directory in one step (`cd ~` or just `cd`)

### Using paths in combination with shell commands

- Directory structure can also be used to specify locations or file names for which to operate on!
- `cd ~` takes me to my home directory
- `pwd` shows absolute path to my current location (home)
- `pwd ..` shows absolute path to directory one level up
- `ls ..` lists files in directory one level up
- `cd ..` moves me up to that directory
- `ls` shows the list of files from within that directory

### Creating a file or a directory
- `touch path/to/<filename>` creates a file (with an optional path statement before it)
- `mkdir` makes a directory in the current directory

### Removing a file or a directory
- `rm <filename>` removes a file (can't undo this)
- `rmdir <directoryname>` removes a directory (directory must be empty)
- `rm -r <directoryname>` removes directory and recursively removes all of its subdirectories and files!

### Copying or moving files, folders, or directories
- `cp sourceFile destinationFile` copies file, folder or directory from source location to somewhere else
- `mv sourceFile destinationFile` moves file, folder or directory from source location to somewhere else

### Renaming or save as... files, folders, or directories
- `mv oldName newName` in same location renames file
- `cp oldName newName` in same location saves a copy of the file to a new name

### Using wildcards
- `rm *.txt` removes all .txt files
- `rm F*.txt` removes all .txt files that begin with the letter F

### Modifying the shell (in Mac)
- go to home in the shell
- look for file `.bash_profile`
- be sure to show hidden files from finder to see this
- if not there, create it in your home with a text editor
- save it to your home area

### Nick's `.bash_profile`
```
# execute these commands when the shell is opened
echo "--> Executed Nick's .bash_profile file"
export BASH_SILENCE_DEPRECATION_WARNING=1
alias ls='ls -GF'
PS1="$ "
export PATH="$PATH:$HOME/Dropbox/shellScripts"
source myAliases.sh
```

### Nick's aliases
```
#!/bin/bash
# Collection of useful bash aliases
# Add aliases and then source this file

# directory aliases
alias desk="cd ~/Desktop"
alias dropbox="cd ~/Dropbox"
alias repo="cd ~//Desktop/githubRepos"

# alias for editing this file
alias myalias="cd ~;vim myAliases.sh"

# new alias for git log
alias glog="git log --oneline -6"

# function gitgo for all git commands
gitgo(){
  git add -A
  git commit -m "$1"
  git push
  git status 
}
```
### Creating your own shell scripts
- modify path statement in your `.bash_profile` to point to a directory where your shell scripts will be stored: `export PATH="$PATH:$HOME/Dropbox/shellScripts"`
- go to the directory and create this script called `trialScript.sh`. Use the `sh` suffix to remind you that this is a shell script
- using your plaintext editor, issue these commands inside your shell script:
```
# Minimal shell script
#! /bin/bash
<<<<<<< HEAD
echo '++++++++++++++++++++++++'
echo 'Trial shell script'
echo 'current date and time: '
date
echo 'current directory: '
pwd
echo 'directory contents: '
ls -AFG
echo '++++++++++++++++++++++++'

```
- be sure to include a final carriage return at the end of the last line:
- change the permissions of the file so it can be executed as a script in bash: `chmod u+x trialScript.sh`

- navigate with the shell to different locations and run the script by typing `trialScript.sh`

- any new scripts should be placed in this same location and will need their permissions changed before they will work

```
echo `++++++++++++++++++++++++`
echo `Trial shell script`
echo `current date and time:
date
echo `current directory: `
pwd
echo `directory contents: `
ls -AFG
echo `++++++++++++++++++++++++`
```
- change the permissions of the file so it can be executed as a script in bash: `chmod u+x trialScript.sh`

- navigate with the shell to different locations and run the script by typing `trialScript.sh`