Basic Bash

Learning Objectives

• Open up the terminal.
• Basic shell commands.
• Chapter 4 of Git for Scientists.
• Terminus.

The Command Line

• The command line is like the R command prompt: you insert code, hit enter, and then the computer executes your command.

• However, instead of inserting R code, you insert Shell Script.

• In this class, we will use the command line primarily for two things:

  • Moving around your file system.
  • Running git commands.

• Other words for command line: shell, terminal, command line interface (cli), and console.

  • These terms are technically slightly different.

• There are many types of shells, each with their own scripting language. We will use the bash scripting language for this class.

• A huge difference between R and bash is how commands/functions are called.

  • R: f(x, y = 1)
  • Bash: f x --y=1
  • Arguments that are “flags” use only one dash, like f x -g would incorporate the g flag.

• If you are using Linux or Mac, then you can keep going. If you are using Windows, you need to first download and install git (and thus git bash) from here: http://git-scm.com/download/win. You might need to restart R Studio if you are already running it.

• Open up the terminal

  • Windows: Open up the Git Bash app. It should look like this:

    

  • Mac: On your Mac, do one of the following:

    • Click the Launchpad icon in the Dock, type Terminal in the search field, then click Terminal.
    • In the Finder , open the /Applications/Utilities folder, then double-click Terminal.

  • Ubuntu: Do one of the following

    • Open the dash and search for “terminal”. Open up the terminal.

    • Use keyboard shortcut: Ctrl+Alt+T

    • It should look like this:

      

• All commands get placed after the dollar sign.

• The path before the dollar sign is the working directory of the terminal, not R’s working directory. It’s where the shell will reference all files from.

• The tilde “~” is shorthand for the “home directory”. Each computer has a home directory that is the “default directory”.

Useful Commands:

• pwd: Print working directory. Show the current working directory. This is like getwd() in R.

  pwd

  /home/dgerard/Dropbox/teaching/stat_413_613/lectures/01_git

• ls: List the current files and folders in a directory.

  ls

  01_basic_bash.Rmd
  01_figs
  01_git_branch.Rmd
  01_git_github.Rmd
  01_git_lfs.Rmd
  01_git_setup.Rmd
  blischak_etal_2016.PDF
  citation.bib
  graphics

• cd: Change directories. This is like setwd() in R. As when we specified paths in R, using two periods mean “move back a folder”.

  cd ../
  pwd

  /home/dgerard/Dropbox/teaching/stat_413_613/lectures

  • If you use cd without specifying a folder to move to, it will move the working directory to the home directory.

  cd
  pwd

  /home/dgerard

  • OK, I’m going to move us back to the 01_git directory.

  cd ./Dropbox/teaching/data_496_696/lectures/01_git

• man: Read the manual of a command. Just like help() in R.

  man ls

  • This will open up the man page of ls. You can scroll through this page using the up and down arrows. You can exit this page by typing q.

  • This won’t work for Git Bash (for Windows users). Instead, you’ll need to type

    ls --help

• Exercise: What is your home directory? What files/folders exist in your home directory? Navigate to it and then navigate back to your notes.

• Exercise: Where does the following command take you? How does it work?

  cd ~/../../..

• Exercise: Read the manual page of ls. What does the a flag do? Try it out!

Other commands.

• touch: Create an empty file.

  touch empty_file.txt

• more: Open up a preview of a document. You can exit the preview by typeing q.

  more 01_basic_bash.Rmd 

• cp: Copy a file.

  cp 01_basic_bash.Rmd hellobash.Rmd
  ls

  01_basic_bash.Rmd
  01_figs
  01_git_branch.Rmd
  01_git_github.Rmd
  01_git_lfs.Rmd
  01_git_setup.Rmd
  blischak_etal_2016.PDF
  citation.bib
  graphics
  hellobash.Rmd

• mv: Move/rename a file.

  mv hellobash.Rmd goodbyebash.Rmd
  ls

  01_basic_bash.Rmd
  01_figs
  01_git_branch.Rmd
  01_git_github.Rmd
  01_git_lfs.Rmd
  01_git_setup.Rmd
  blischak_etal_2016.PDF
  citation.bib
  goodbyebash.Rmd
  graphics

• rm: Remove a file.

  rm goodbyebash.Rmd
  ls

  01_basic_bash.Rmd
  01_figs
  01_git_branch.Rmd
  01_git_github.Rmd
  01_git_lfs.Rmd
  01_git_setup.Rmd
  blischak_etal_2016.PDF
  citation.bib
  graphics

• mkdir: Make a directory/folder.

  mkdir tempdir
  ls

  01_basic_bash.Rmd
  01_figs
  01_git_branch.Rmd
  01_git_github.Rmd
  01_git_lfs.Rmd
  01_git_setup.Rmd
  blischak_etal_2016.PDF
  citation.bib
  graphics
  tempdir

• rmdir: Remove a directory/folder.

  rmdir tempdir
  ls

  01_basic_bash.Rmd
  01_figs
  01_git_branch.Rmd
  01_git_github.Rmd
  01_git_lfs.Rmd
  01_git_setup.Rmd
  blischak_etal_2016.PDF
  citation.bib
  graphics

String search with grep

Find any string in any file in the current working directory (or subdirectories or the current working directory).

• -r recursive
• -n line number
• -w whole word only
• -e pattern
• pdfgrep (need to install separately) for searching text in PDFs.

grep -rnw -e "move"

01_basic_bash.Rmd:93:  paths in R, using two periods mean "move back a folder". 
01_basic_bash.Rmd:100:    - If you use `cd` without specifying a folder to move to, it will move the 
01_basic_bash.Rmd:108:    - OK, I'm going to move us back to the 01_git directory.  
01_basic_bash.Rmd:200:grep -rnw -e "move"
01_git_github.Rmd:69:- You can go back to previous versions of your code/text, then move forward to 
01_git_github.Rmd:226:- Then move into your new repo
.Rhistory:2:grep -rnwe "move"

grep -rnw -e "mov"

01_basic_bash.Rmd:204:grep -rnw -e "mov"
01_basic_bash.Rmd:208:grep -rn -e "mov"

grep -rn -e "mov"

01_basic_bash.Rmd:93:  paths in R, using two periods mean "move back a folder". 
01_basic_bash.Rmd:100:    - If you use `cd` without specifying a folder to move to, it will move the 
01_basic_bash.Rmd:108:    - OK, I'm going to move us back to the 01_git directory.  
01_basic_bash.Rmd:168:- `rm`: Remove a file.
01_basic_bash.Rmd:182:- `rmdir`: Remove a directory/folder.
01_basic_bash.Rmd:200:grep -rnw -e "move"
01_basic_bash.Rmd:204:grep -rnw -e "mov"
01_basic_bash.Rmd:208:grep -rn -e "mov"
01_basic_bash.Rmd:233:I'll remove that file now
01_git_github.Rmd:69:- You can go back to previous versions of your code/text, then move forward to 
01_git_github.Rmd:226:- Then move into your new repo
01_git_github.Rmd:398:- Lines after a "`+`" are being added. Lines after a "`-`" are being removed.
.Rhistory:2:grep -rnwe "move"
.Rhistory:9:conda_remove(envname = "r-reticulate")
.Rhistory:11:conda_remove("bs4")

Download data with wget

Non-interactive downloading of data.

Not available for Git Bash for Windows.

• -nc Don’t download new copies if already there.
• -nd Put all files in current working directory.
• -P Tell where to download the files. Default is current working directory (.)
• -r Recursive downloading. Download all files in the directory up to a certain level.
• l Determine the level for recursive downloading.

E.g. to download the HTML file that contains the Wikipedia list of theological demons, we can go

wget -nc -nd https://en.wikipedia.org/wiki/List_of_theological_demons

--2022-11-16 13:29:02--  https://en.wikipedia.org/wiki/List_of_theological_demons
Resolving en.wikipedia.org (en.wikipedia.org)... 208.80.154.224, 2620:0:861:ed1a::1
Connecting to en.wikipedia.org (en.wikipedia.org)|208.80.154.224|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 79328 (77K) [text/html]
Saving to: ‘List_of_theological_demons’

     0K .......... .......... .......... .......... .......... 64% 15.2M 0s
    50K .......... .......... .......                         100% 22.6M=0.004s

2022-11-16 13:29:02 (17.2 MB/s) - ‘List_of_theological_demons’ saved [79328/79328]

ls

01_basic_bash.Rmd
01_figs
01_git_branch.Rmd
01_git_github.Rmd
01_git_lfs.Rmd
01_git_setup.Rmd
blischak_etal_2016.PDF
citation.bib
graphics
List_of_theological_demons

I’ll remove that file now

rm List_of_theological_demons

Search your command history with reverse-i-search

1. ctrl+r to get search prompt
2. Type a search term
3. ctrl+r to cycle through matches
4. Hit enter if you want to reuse the match. Hit ctrl+c to exit out of the search.