shell_cheatsheet.md

   1 # Basic Shell Commands
   2 ***
   3
   4 ## 1. Shell Basics:
   5
   6 | Command        | Definition                                                                                                     |
   7 |----------------|----------------------------------------------------------------------------------------------------------------|
   8 | `.`            | a single period refers to the current directory                                                                |
   9 | `..`           | a double period refers to the directory immediately above the current directory                                |
  10 | `~`            | refers to your home directory. _Note:_ this command does NOT work on Windows machines (Mac and Linux are okay) |
  11 | `cd ./dirname` | changes the current directory to the directory `dirname`                                                       |
  12 | `ls -F`        | tells you what files and directories are in the current directory                                              |
  13
  14
  15
  16 ## 2. Creating Things:
  17 ### a) How to create new files and directories..
  18
  19 | Command           | Definition                                                                                                                                                                                                                                                                                                                                            |
  20 |-------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
  21 | `mkdir ./dirname` | makes a new directory called dirname below the current directory. _Note:_ Windows users will need to use `\` instead of `/` for the path separator                                                                                                                                                                                                    |
  22 | `nano filename`   | if `filename` does not exist, `nano` creates it and opens the `nano` text editor. If the file exists, `nano` opens it. _Note:_ _(i)_ You can use a different text editor if you like.  In gnome Linux, `gedit` works really well too. _(ii)_ `nano` (or `gedit`) create text files. It doesn't matter what the file extension is (or if there is one) |
  23
  24 ### b) How to delete files and directories...
  25 #### _Remember that deleting is forever. There is NO going back_
  26
  27 | Command           | Definition                                                                                                       |
  28 |-------------------|------------------------------------------------------------------------------------------------------------------|
  29 | `rm ./filename`   | deletes a file called `filename` from the current directory                                                      |
  30 | `rmdir ./dirname` |  deletes the directory `dirname` from the current directory. _Note:_ `dirname` must be empty for `rmdir` to run. |
  31
  32 ### c) How to copy and rename files and directories...
  33
  34 | Command | Definition                                                                                                                                                                                                                    |
  35 |---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
  36 | `mv tmp/filename .` | moves the file `filename` from the directory `tmp` to the current directory. _Note:_ _(i)_ the original `filename` in `tmp` is deleted. _(ii)_ `mv` can also be used to rename files (e.g., `mv filename newname` |
  37 | `cp tmp/filename .` | copies the file `filename` from the directory `tmp` to the current directory. _Note:_ _(i)_ the original file is still there                                                                                      |
  38
  39
  40
  41 ## 3. Pipes and Filters
  42 ### a) How to use wildcards to match filenames...
  43 Wildcards are a shell feature that makes the command line much more powerful than any GUI file managers.
  44 Wildcards are particularly useful when you are looking for directories, files, or file content that can
  45 vary along a given dimension.  These wildcards can be used with any command that accepts file names or
  46 text strings as arguments.
  47
  48 #### Table of commonly used wildcards
  49
  50 | Wildcard               | Matches                                        |
  51 |------------------------|------------------------------------------------|
  52 | `*`                    | zero or more characters                        |
  53 | `?`                    | exactly one character                          |
  54 | `[abcde]`              | exactly one of the characters listed           |
  55 | `[a-e]`                | exactly one character in the given range       |
  56 | `[!abcde]`             | any character not listed                       |
  57 | `[!a-e]`               | any character that is not in the given range   |
  58 | `{software,carpentry}` | exactly one entire word from the options given |
  59
  60 See the cheatsheet on regular expressions for more "wildcard" shortcuts.
  61
  62 ### b) How to redirect to a file and get input from a file ...
  63 Redirection operators can be used to redirect the ouput from a program from the display screen to a file where it is saved (or many other places too, like your printer or to another program where it can be used as input).
  64
  65
  66 | Command | Description                                                                                                                     |
  67 |---------|---------------------------------------------------------------------------------------------------------------------------------|
  68 | `>`     | write `stdout` to a new file; overwrites any file with that name (e.g., `ls *.md > mardkownfiles.txt`)                          |
  69 | `>>`    | append `stdout` to a previously existing file; if the file does not exist, it is created (e.g., `ls *.md >> markdownfiles.txt`) |
  70 | `<`     | assigns the information in a file to a variable, loop, etc (e.g., `n < markdownfiles.md`)                                       |
  71
  72
  73
  74 #### b.1) How to use the output of one command as the input to another with a pipe...
  75 A special kind of redirection is called a pipe and is denoted by `|`.
  76
  77
  78 | Command | Description                                                                                                                                           |
  79 |---------|-------------------------------------------------------------------------------------------------------------------------------------------------------|
  80 | &#124;     | Output from one command line program can be used as input to another one (e.g. ls \*.md &#124; head gives you the first 5 `*.md` files in your directory) |
  81
  82
  83
  84
  85
  86 ##### Example:
  87
  88     ls *.md | head | sed -i `s/markdown/software/g`
  89
  90 changes all the instances of the word `markdown` to `software` in the first 5 `*.md` files in your current directory.
  91
  92
  93
  94
  95 ## 4. How to repeat operations using a loop...
  96 Loops assign a value in a list or counter to a variable that takes on a different value each time through the loop.
  97 There are 2 primary kinds of loops: `for` loops and `while` loops.
  98
  99 ### a) For loop
 100 For loops loop through variables in a list
 101
 102
 103     for varname in list
 104     do
 105         command 1
 106         command 2
 107     done
 108
 109 where,
 110
 111 *  `for`, `in`, `do`, and `done` are keywords
 112 *  `list` contains a list of values separated by spaces. e.g. `list` can be replaced by `1 2 3 4 5 6` or by `Bob Mary Sue Greg`. `list` can also be a variable:
 113
 114 --
 115
 116     list[0]=Sam
 117     list[1]=Lynne
 118     list[2]=Dhavide
 119     list[3]=Trevor
 120     .
 121     .
 122     .
 123     list[n]=Mark
 124
 125 which is referenced in the loop by:
 126
 127     for varname in ${list[@]}
 128     do
 129         command 1
 130         command 2
 131     done
 132
 133
 134 _Note:_ Bash is zero indexed, so counting always starts at `0`, not `1`.
 135
 136
 137 ### b) While Loop
 138 While loops loop through the commands until a condition is met. For example
 139
 140     COUNTER=0
 141     while [ ${COUNTER} -lt 10 ]; do
 142         command 1
 143         command 2
 144         COUNTER=`expr ${COUNTER} + 1`
 145     done
 146
 147 continues the loop as long as the value in the variable COUNTER is less than 10 (incremented by 1 on each iteration of the loop).
 148
 149 *  `while`, `do`, and `done` are keywords
 150
 151
 152 #### b.1) Commonly used conditional operators
 153
 154 | Operator | Definition               |
 155 |----------|--------------------------|
 156 | `-eq`    | is equal to              |
 157 | `-ne`    | is not equal to          |
 158 | `-gt`    | greater than             |
 159 | `-ge`    | greater than or equal to |
 160 | `-lt`    | less than                |
 161 | `-le`    | less than or equal to    |
 162
 163
 164
 165
 166
 167 ## 6. Finding Things
 168 ### a) How to select lines matching patterns in text files...
 169 To find information within files, you use a command called `grep`.
 170
 171 | Example command                | Description                                                                                    |
 172 |--------------------------------|------------------------------------------------------------------------------------------------|
 173 | `grep [options] day haiku.txt` | finds every instance of the string `day` in the file haiku.txt and pipes it to standard output |                                                                                                                                                                                                                |
 174
 175 #### a.1) Commonly used `grep` options
 176
 177 |      | `grep` options                                                                                                                                                                                                       |
 178 |------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 179 | `-E` | tells grep you will be using a regular expression. Enclose the regular expression in quotes. _Note:_ the power of `grep` comes from using regular expressions. Please see the regular expressions sheet for examples |
 180 | `-i` | makes matching case-insensitive                                                                                                                                                                                      |
 181 | `-n` | limits the number of lines that match to the first n matches                                                                                                                                                         |
 182 | `-v` | shows lines that do not match the pattern (inverts the match)                                                                                                                                                        |
 183 | `-w` | outputs instances where the pattern is a whole word                                                                                                                                                                  |
 184
 185 ### b) How to find files with certain properties...
 186 To find file and directory names, you use a command called `find`
 187
 188 | Example command  | Description |
 189 |------------------|-------------|
 190 | `find . -type d` | `find` recursively descends the directory tree for each path listed to match the expression given in the command line with file or directory names in the search path |
 191
 192
 193 #### b.1) Commonly used `find` options
 194
 195 |               | `find` options                                                                                                                                          |
 196 |---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|
 197 | `-type [df]`  | `d` lists directories; `f` lists files                                                                                                                  |
 198 | `-maxdepth n` | `find` automatically searches subdirectories. If you don't want that, specify the number of levels below the working directory you would like to search |
 199 | `-mindepth n` | starts `find`'s search `n` levels below the working directory                                                                                           |
 200
 201