# Navigating Files and Directories

The part of the operating system responsible for managing files and directories is called the file system. It organizes our data into files, which hold information, and directories (also called “folders”), which hold files or other directories.

Several commands are frequently used to create, inspect, rename, and delete files and directories. To start exploring them, we’ll go to our open shell window.

First let’s find out where we are by running a command called pwd (which stands for “print working directory”). Directories are like places - at any time while we are using the shell we are in exactly one place, called our current working directory. Commands mostly read and write files in the current working directory, i.e. “here”, so knowing where you are before running a command is important. pwd shows you where you are:

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks/01-bash



Here, the computer’s response is /Users/nelle, which is Nelle’s home directory.

## Home Directory Variation

The home directory path will look different on different operating systems. On Linux it may look like /home/nelle, and on Windows it will be similar to C:\Documents and Settings\nelle or C:\Users\nelle.
(Note that it may look slightly different for different versions of Windows.) In future examples, we've used Mac output as the default - Linux and Windows output may differ slightly, but should be generally similar.

To understand what a “home directory” is, let’s have a look at how the file system as a whole is organized. For the sake of this example, we’ll be illustrating the filesystem on our scientist Nelle’s computer. After this illustration, you’ll be learning commands to explore your own filesystem, which will be constructed in a similar way, but not be exactly identical.

On Nelle’s computer, the filesystem looks like this:

At the top is the root directory that holds everything else. We refer to it using a slash character, /, on its own; this is the leading slash in /Users/nelle.

Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (for miscellaneous data files), Users (where users’ personal directories are located), tmp (for temporary files that don’t need to be stored long-term), and so on.

We know that our current working directory /Users/nelle is stored inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.

## Slashes

Notice that there are two meanings for the / character. When it appears at the front of a file or directory name, it refers to the root directory. When it appears inside a name, it's just a separator.

Underneath /Users, we find one directory for each user with an account on Nelle’s machine, her colleagues the Mummy and Wolfman.

The Mummy’s files are stored in /Users/imhotep, Wolfman’s in /Users/larry, and Nelle’s in /Users/nelle. Because Nelle is the user in our examples here, this is why we get /Users/nelle as our home directory.
Typically, when you open a new command prompt you will be in your home directory to start.

Now let’s learn the command that will let us see the contents of our own filesystem. We can see what’s in our home directory by running ls, which stands for “listing”:

ls

01-introducing-the-shell_instructor.ipynb
01-introducing-the-shell.ipynb
02-files-and-directories_instructor.ipynb
02-files-and-directories.ipynb
03-working-with-files-and-directories_instructor.ipynb
03-working-with-files-and-directories.ipynb
filesystem-challenge.svg
filesystem.svg
home-directories.svg
nano-screenshot.png
thesis



(Again, your results may be slightly different depending on your operating system and how you have customized your filesystem.)

ls prints the names of the files and directories in the current directory. We can make its output more comprehensible by using the flag -F (also known as a switch or an option) , which tells ls to add a marker to file and directory names to indicate what they are. A trailing / indicates that this is a directory. Depending on your settings, it might also use colors to indicate whether each entry is a file or directory. You might recall that we used ls -F in an earlier example.

ls -F

01-introducing-the-shell_instructor.ipynb
01-introducing-the-shell.ipynb
02-files-and-directories_instructor.ipynb
02-files-and-directories.ipynb
03-working-with-files-and-directories_instructor.ipynb
03-working-with-files-and-directories.ipynb
filesystem-challenge.svg
filesystem.svg
home-directories.svg
nano-screenshot.png
thesis/



### Getting help

ls has lots of other flags. There are two common ways to find out how to use a command and what flags it accepts:

1. We can pass a --help flag to the command, such as:
ls --help

Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options too.
-a, --all                  do not ignore entries starting with .
-A, --almost-all           do not list implied . and ..
--author               with -l, print the author of each file
-b, --escape               print C-style escapes for nongraphic characters
--block-size=SIZE      with -l, scale sizes by SIZE when printing them;
e.g., '--block-size=M'; see SIZE format below
-B, --ignore-backups       do not list implied entries ending with ~
-c                         with -lt: sort by, and show, ctime (time of last
modification of file status information);
with -l: show ctime and sort by name;
otherwise: sort by ctime, newest first
-C                         list entries by columns
--color[=WHEN]         colorize the output; WHEN can be 'always' (default
-d, --directory            list directories themselves, not their contents
-D, --dired                generate output designed for Emacs' dired mode
-f                         do not sort, enable -aU, disable -ls --color
-F, --classify             append indicator (one of */=>@|) to entries
--file-type            likewise, except do not append '*'
--format=WORD          across -x, commas -m, horizontal -x, long -l,
single-column -1, verbose -l, vertical -C
--full-time            like -l --time-style=full-iso
-g                         like -l, but do not list owner
--group-directories-first
group directories before files;
can be augmented with a --sort option, but any
use of --sort=none (-U) disables grouping
-G, --no-group             in a long listing, don't print group names
-h, --human-readable       with -l and -s, print sizes like 1K 234M 2G etc.
--si                   likewise, but use powers of 1000 not 1024
-H, --dereference-command-line
that points to a directory
--hide=PATTERN         do not list implied entries matching shell PATTERN
(overridden by -a or -A)
(default if omitted), 'auto', or 'never'
--indicator-style=WORD  append indicator with style WORD to entry names:
none (default), slash (-p),
file-type (--file-type), classify (-F)
-i, --inode                print the index number of each file
-I, --ignore=PATTERN       do not list implied entries matching shell PATTERN
-k, --kibibytes            default to 1024-byte blocks for disk usage;
used only with -s and per directory totals
-l                         use a long listing format
-L, --dereference          when showing file information for a symbolic
references rather than for the link itself
-m                         fill width with a comma separated list of entries
-n, --numeric-uid-gid      like -l, but list numeric user and group IDs
-N, --literal              print entry names without quoting
-o                         like -l, but do not list group information
-p, --indicator-style=slash
append / indicator to directories
-q, --hide-control-chars   print ? instead of nongraphic characters
--show-control-chars   show nongraphic characters as-is (the default,
unless program is 'ls' and output is a terminal)
-Q, --quote-name           enclose entry names in double quotes
--quoting-style=WORD   use quoting style WORD for entry names:
literal, locale, shell, shell-always,
shell-escape, shell-escape-always, c, escape
(overrides QUOTING_STYLE environment variable)
-r, --reverse              reverse order while sorting
-R, --recursive            list subdirectories recursively
-s, --size                 print the allocated size of each file, in blocks
-S                         sort by file size, largest first
--sort=WORD            sort by WORD instead of name: none (-U), size (-S),
time (-t), version (-v), extension (-X)
--time=WORD            with -l, show time as WORD instead of default
modification time: atime or access or use (-u);
ctime or status (-c); also use specified time
as sort key if --sort=time (newest first)
--time-style=TIME_STYLE  time/date format with -l; see TIME_STYLE below
-t                         sort by modification time, newest first
-T, --tabsize=COLS         assume tab stops at each COLS instead of 8
-u                         with -lt: sort by, and show, access time;
with -l: show access time and sort by name;
otherwise: sort by access time, newest first
-U                         do not sort; list entries in directory order
-v                         natural sort of (version) numbers within text
-w, --width=COLS           set output width to COLS.  0 means no limit
-x                         list entries by lines instead of by columns
-X                         sort alphabetically by entry extension
-Z, --context              print any security context of each file
-1                         list one file per line.  Avoid '\n' with -q or -b
--help     display this help and exit
--version  output version information and exit

The SIZE argument is an integer and optional unit (example: 10K is 10*1024).
Units are K,M,G,T,P,E,Z,Y (powers of 1024) or KB,MB,... (powers of 1000).

The TIME_STYLE argument can be full-iso, long-iso, iso, locale, or +FORMAT.
FORMAT is interpreted like in date(1).  If FORMAT is FORMAT1<newline>FORMAT2,
then FORMAT1 applies to non-recent files and FORMAT2 to recent files.
TIME_STYLE prefixed with 'posix-' takes effect only outside the POSIX locale.
Also the TIME_STYLE environment variable sets the default style to use.

Using color to distinguish file types is disabled both by default and
with --color=never.  With --color=auto, ls emits color codes only when
standard output is connected to a terminal.  The LS_COLORS environment
variable can change the settings.  Use the dircolors command to set it.

Exit status:
0  if OK,
1  if minor problems (e.g., cannot access subdirectory),
2  if serious trouble (e.g., cannot access command-line argument).

Full documentation at: <https://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'


1. We can read its manual with man, such as:
man ls

LS(1)                            User Commands                           LS(1)

[1mNAME[0m
ls - list directory contents

[1mSYNOPSIS[0m
[1mls [22m[[4mOPTION[24m]... [[4mFILE[24m]...

[1mDESCRIPTION[0m
List  information  about  the FILEs (the current directory by default).
Sort entries alphabetically if none of [1m-cftuvSUX [22mnor [1m--sort  [22mis  speci‐
fied.

Mandatory  arguments  to  long  options are mandatory for short options
too.

[1m-a[22m, [1m--all[0m
do not ignore entries starting with .

[1m-A[22m, [1m--almost-all[0m
do not list implied . and ..

[1m--author[0m
with [1m-l[22m, print the author of each file

[1m-b[22m, [1m--escape[0m
print C-style escapes for nongraphic characters

[1m--block-size[22m=[4mSIZE[0m
with  [1m-l[22m,  scale  sizes  by  SIZE  when  printing  them;   e.g.,
'--block-size=M'; see SIZE format below

[1m-B[22m, [1m--ignore-backups[0m
do not list implied entries ending with ~

[1m-c     [22mwith [1m-lt[22m: sort by, and show, ctime (time of last modification of
file status information); with [1m-l[22m: show ctime and sort by  name;
otherwise: sort by ctime, newest first

[1m-C     [22mlist entries by columns

[1m--color[22m[=[4mWHEN[24m]
colorize  the output; WHEN can be 'always' (default if omitted),

[1m-d[22m, [1m--directory[0m
list directories themselves, not their contents

[1m-D[22m, [1m--dired[0m
generate output designed for Emacs' dired mode

[1m-f     [22mdo not sort, enable [1m-aU[22m, disable [1m-ls --color[0m

[1m-F[22m, [1m--classify[0m
append indicator (one of */=>@|) to entries

[1m--file-type[0m
likewise, except do not append '*'

[1m--format[22m=[4mWORD[0m
across [1m-x[22m, commas [1m-m[22m, horizontal [1m-x[22m, long [1m-l[22m, single-column  [1m-1[22m,
verbose [1m-l[22m, vertical [1m-C[0m

[1m--full-time[0m
like [1m-l --time-style[22m=[4mfull-iso[0m

[1m-g     [22mlike [1m-l[22m, but do not list owner

[1m--group-directories-first[0m
group directories before files;

can   be  augmented  with  a  [1m--sort  [22moption,  but  any  use  of
[1m--sort[22m=[4mnone[24m ([1m-U[22m) disables grouping

[1m-G[22m, [1m--no-group[0m
in a long listing, don't print group names

with [1m-l [22mand [1m-s[22m, print sizes like 1K 234M 2G etc.

[1m--si   [22mlikewise, but use powers of 1000 not 1024

[1m-H[22m, [1m--dereference-command-line[0m

that points to a directory

[1m--hide[22m=[4mPATTERN[0m
do not list implied entries matching shell  PATTERN  (overridden
by [1m-a [22mor [1m-A[22m)

hyperlink file names; WHEN can be 'always' (default if omitted),
'auto', or 'never'

[1m--indicator-style[22m=[4mWORD[0m
append indicator with style WORD to entry names: none (default),
slash ([1m-p[22m), file-type ([1m--file-type[22m), classify ([1m-F[22m)

[1m-i[22m, [1m--inode[0m
print the index number of each file

[1m-I[22m, [1m--ignore[22m=[4mPATTERN[0m
do not list implied entries matching shell PATTERN

[1m-k[22m, [1m--kibibytes[0m
default  to  1024-byte  blocks for disk usage; used only with [1m-s[0m
and per directory totals

[1m-l     [22muse a long listing format

[1m-L[22m, [1m--dereference[0m
when showing file information for a symbolic link, show informa‐
tion  for  the file the link references rather than for the link
itself

[1m-m     [22mfill width with a comma separated list of entries

[1m-n[22m, [1m--numeric-uid-gid[0m
like [1m-l[22m, but list numeric user and group IDs

[1m-N[22m, [1m--literal[0m
print entry names without quoting

[1m-o     [22mlike [1m-l[22m, but do not list group information

[1m-p[22m, [1m--indicator-style[22m=[4mslash[0m
append / indicator to directories

[1m-q[22m, [1m--hide-control-chars[0m
print ? instead of nongraphic characters

[1m--show-control-chars[0m
show nongraphic characters as-is (the default, unless program is
'ls' and output is a terminal)

[1m-Q[22m, [1m--quote-name[0m
enclose entry names in double quotes

[1m--quoting-style[22m=[4mWORD[0m
use  quoting style WORD for entry names: literal, locale, shell,
shell-always,  shell-escape,  shell-escape-always,   c,   escape
(overrides QUOTING_STYLE environment variable)

[1m-r[22m, [1m--reverse[0m
reverse order while sorting

[1m-R[22m, [1m--recursive[0m
list subdirectories recursively

[1m-s[22m, [1m--size[0m
print the allocated size of each file, in blocks

[1m-S     [22msort by file size, largest first

[1m--sort[22m=[4mWORD[0m
sort  by  WORD instead of name: none ([1m-U[22m), size ([1m-S[22m), time ([1m-t[22m),
version ([1m-v[22m), extension ([1m-X[22m)

[1m--time[22m=[4mWORD[0m
with [1m-l[22m, show time as WORD instead of default modification time:
atime  or  access  or  use  ([1m-u[22m); ctime or status ([1m-c[22m); also use
specified time as sort key if [1m--sort[22m=[4mtime[24m (newest first)

[1m--time-style[22m=[4mTIME_STYLE[0m
time/date format with [1m-l[22m; see TIME_STYLE below

[1m-t     [22msort by modification time, newest first

[1m-T[22m, [1m--tabsize[22m=[4mCOLS[0m
assume tab stops at each COLS instead of 8

[1m-u     [22mwith [1m-lt[22m: sort by, and show, access time; with [1m-l[22m:  show  access
time  and  sort  by name; otherwise: sort by access time, newest
first

[1m-U     [22mdo not sort; list entries in directory order

[1m-v     [22mnatural sort of (version) numbers within text

[1m-w[22m, [1m--width[22m=[4mCOLS[0m
set output width to COLS.  0 means no limit

[1m-x     [22mlist entries by lines instead of by columns

[1m-X     [22msort alphabetically by entry extension

[1m-Z[22m, [1m--context[0m
print any security context of each file

[1m-1     [22mlist one file per line.  Avoid '\n' with [1m-q [22mor [1m-b[0m

[1m--help [22mdisplay this help and exit

[1m--version[0m
output version information and exit

The SIZE argument is an integer and  optional  unit  (example:  10K  is
10*1024).   Units  are  K,M,G,T,P,E,Z,Y  (powers  of 1024) or KB,MB,...
(powers of 1000).

The TIME_STYLE argument can be  full-iso,  long-iso,  iso,  locale,  or
+FORMAT.   FORMAT  is  interpreted  like in date(1).  If FORMAT is FOR‐
MAT1<newline>FORMAT2, then FORMAT1 applies to non-recent files and FOR‐
MAT2  to  recent files.  TIME_STYLE prefixed with 'posix-' takes effect
only outside the POSIX locale.  Also the TIME_STYLE  environment  vari‐
able sets the default style to use.

Using  color  to distinguish file types is disabled both by default and
with [1m--color[22m=[4mnever[24m.  With [1m--color[22m=[4mauto[24m, ls emits color codes only  when
standard  output is connected to a terminal.  The LS_COLORS environment
variable can change the settings.  Use the dircolors command to set it.

[1mExit status:[0m
0      if OK,

1      if minor problems (e.g., cannot access subdirectory),

2      if serious trouble (e.g., cannot access command-line argument).

[1mAUTHOR[0m
Written by Richard M. Stallman and David MacKenzie.

[1mREPORTING BUGS[0m
Report ls translation bugs to <https://translationproject.org/team/>

GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This  is  free  software:  you  are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Full documentation at: <https://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'

GNU coreutils 8.29               December 2017                           LS(1)



Depending on your environment you might find that only one of these works (either man or --help). We’ll describe both ways below.

#### The --help flag

Many bash commands, and programs that people have written that can be run from within bash, support a --help flag to display more information on how to use the command or program.

ls --help

Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options too.
-a, --all                  do not ignore entries starting with .
-A, --almost-all           do not list implied . and ..
--author               with -l, print the author of each file
-b, --escape               print C-style escapes for nongraphic characters
--block-size=SIZE      with -l, scale sizes by SIZE when printing them;
e.g., '--block-size=M'; see SIZE format below
-B, --ignore-backups       do not list implied entries ending with ~
-c                         with -lt: sort by, and show, ctime (time of last
modification of file status information);
with -l: show ctime and sort by name;
otherwise: sort by ctime, newest first
-C                         list entries by columns
--color[=WHEN]         colorize the output; WHEN can be 'always' (default
-d, --directory            list directories themselves, not their contents
-D, --dired                generate output designed for Emacs' dired mode
-f                         do not sort, enable -aU, disable -ls --color
-F, --classify             append indicator (one of */=>@|) to entries
--file-type            likewise, except do not append '*'
--format=WORD          across -x, commas -m, horizontal -x, long -l,
single-column -1, verbose -l, vertical -C
--full-time            like -l --time-style=full-iso
-g                         like -l, but do not list owner
--group-directories-first
group directories before files;
can be augmented with a --sort option, but any
use of --sort=none (-U) disables grouping
-G, --no-group             in a long listing, don't print group names
-h, --human-readable       with -l and -s, print sizes like 1K 234M 2G etc.
--si                   likewise, but use powers of 1000 not 1024
-H, --dereference-command-line
that points to a directory
--hide=PATTERN         do not list implied entries matching shell PATTERN
(overridden by -a or -A)
(default if omitted), 'auto', or 'never'
--indicator-style=WORD  append indicator with style WORD to entry names:
none (default), slash (-p),
file-type (--file-type), classify (-F)
-i, --inode                print the index number of each file
-I, --ignore=PATTERN       do not list implied entries matching shell PATTERN
-k, --kibibytes            default to 1024-byte blocks for disk usage;
used only with -s and per directory totals
-l                         use a long listing format
-L, --dereference          when showing file information for a symbolic
references rather than for the link itself
-m                         fill width with a comma separated list of entries
-n, --numeric-uid-gid      like -l, but list numeric user and group IDs
-N, --literal              print entry names without quoting
-o                         like -l, but do not list group information
-p, --indicator-style=slash
append / indicator to directories
-q, --hide-control-chars   print ? instead of nongraphic characters
--show-control-chars   show nongraphic characters as-is (the default,
unless program is 'ls' and output is a terminal)
-Q, --quote-name           enclose entry names in double quotes
--quoting-style=WORD   use quoting style WORD for entry names:
literal, locale, shell, shell-always,
shell-escape, shell-escape-always, c, escape
(overrides QUOTING_STYLE environment variable)
-r, --reverse              reverse order while sorting
-R, --recursive            list subdirectories recursively
-s, --size                 print the allocated size of each file, in blocks
-S                         sort by file size, largest first
--sort=WORD            sort by WORD instead of name: none (-U), size (-S),
time (-t), version (-v), extension (-X)
--time=WORD            with -l, show time as WORD instead of default
modification time: atime or access or use (-u);
ctime or status (-c); also use specified time
as sort key if --sort=time (newest first)
--time-style=TIME_STYLE  time/date format with -l; see TIME_STYLE below
-t                         sort by modification time, newest first
-T, --tabsize=COLS         assume tab stops at each COLS instead of 8
-u                         with -lt: sort by, and show, access time;
with -l: show access time and sort by name;
otherwise: sort by access time, newest first
-U                         do not sort; list entries in directory order
-v                         natural sort of (version) numbers within text
-w, --width=COLS           set output width to COLS.  0 means no limit
-x                         list entries by lines instead of by columns
-X                         sort alphabetically by entry extension
-Z, --context              print any security context of each file
-1                         list one file per line.  Avoid '\n' with -q or -b
--help     display this help and exit
--version  output version information and exit

The SIZE argument is an integer and optional unit (example: 10K is 10*1024).
Units are K,M,G,T,P,E,Z,Y (powers of 1024) or KB,MB,... (powers of 1000).

The TIME_STYLE argument can be full-iso, long-iso, iso, locale, or +FORMAT.
FORMAT is interpreted like in date(1).  If FORMAT is FORMAT1<newline>FORMAT2,
then FORMAT1 applies to non-recent files and FORMAT2 to recent files.
TIME_STYLE prefixed with 'posix-' takes effect only outside the POSIX locale.
Also the TIME_STYLE environment variable sets the default style to use.

Using color to distinguish file types is disabled both by default and
with --color=never.  With --color=auto, ls emits color codes only when
standard output is connected to a terminal.  The LS_COLORS environment
variable can change the settings.  Use the dircolors command to set it.

Exit status:
0  if OK,
1  if minor problems (e.g., cannot access subdirectory),
2  if serious trouble (e.g., cannot access command-line argument).

Full documentation at: <https://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'



## Unsupported command-line options

If you try to use an option (flag) that is not supported, ls and other programs will usually print an error message similar to:

\$ ls -j

ls: invalid option -- 'j'


## The man command

The other way to learn about ls is to type

man ls

LS(1)                            User Commands                           LS(1)

[1mNAME[0m
ls - list directory contents

[1mSYNOPSIS[0m
[1mls [22m[[4mOPTION[24m]... [[4mFILE[24m]...

[1mDESCRIPTION[0m
List  information  about  the FILEs (the current directory by default).
Sort entries alphabetically if none of [1m-cftuvSUX [22mnor [1m--sort  [22mis  speci‐
fied.

Mandatory  arguments  to  long  options are mandatory for short options
too.

[1m-a[22m, [1m--all[0m
do not ignore entries starting with .

[1m-A[22m, [1m--almost-all[0m
do not list implied . and ..

[1m--author[0m
with [1m-l[22m, print the author of each file

[1m-b[22m, [1m--escape[0m
print C-style escapes for nongraphic characters

[1m--block-size[22m=[4mSIZE[0m
with  [1m-l[22m,  scale  sizes  by  SIZE  when  printing  them;   e.g.,
'--block-size=M'; see SIZE format below

[1m-B[22m, [1m--ignore-backups[0m
do not list implied entries ending with ~

[1m-c     [22mwith [1m-lt[22m: sort by, and show, ctime (time of last modification of
file status information); with [1m-l[22m: show ctime and sort by  name;
otherwise: sort by ctime, newest first

[1m-C     [22mlist entries by columns

[1m--color[22m[=[4mWHEN[24m]
colorize  the output; WHEN can be 'always' (default if omitted),

[1m-d[22m, [1m--directory[0m
list directories themselves, not their contents

[1m-D[22m, [1m--dired[0m
generate output designed for Emacs' dired mode

[1m-f     [22mdo not sort, enable [1m-aU[22m, disable [1m-ls --color[0m

[1m-F[22m, [1m--classify[0m
append indicator (one of */=>@|) to entries

[1m--file-type[0m
likewise, except do not append '*'

[1m--format[22m=[4mWORD[0m
across [1m-x[22m, commas [1m-m[22m, horizontal [1m-x[22m, long [1m-l[22m, single-column  [1m-1[22m,
verbose [1m-l[22m, vertical [1m-C[0m

[1m--full-time[0m
like [1m-l --time-style[22m=[4mfull-iso[0m

[1m-g     [22mlike [1m-l[22m, but do not list owner

[1m--group-directories-first[0m
group directories before files;

can   be  augmented  with  a  [1m--sort  [22moption,  but  any  use  of
[1m--sort[22m=[4mnone[24m ([1m-U[22m) disables grouping

[1m-G[22m, [1m--no-group[0m
in a long listing, don't print group names

with [1m-l [22mand [1m-s[22m, print sizes like 1K 234M 2G etc.

[1m--si   [22mlikewise, but use powers of 1000 not 1024

[1m-H[22m, [1m--dereference-command-line[0m

that points to a directory

[1m--hide[22m=[4mPATTERN[0m
do not list implied entries matching shell  PATTERN  (overridden
by [1m-a [22mor [1m-A[22m)

hyperlink file names; WHEN can be 'always' (default if omitted),
'auto', or 'never'

[1m--indicator-style[22m=[4mWORD[0m
append indicator with style WORD to entry names: none (default),
slash ([1m-p[22m), file-type ([1m--file-type[22m), classify ([1m-F[22m)

[1m-i[22m, [1m--inode[0m
print the index number of each file

[1m-I[22m, [1m--ignore[22m=[4mPATTERN[0m
do not list implied entries matching shell PATTERN

[1m-k[22m, [1m--kibibytes[0m
default  to  1024-byte  blocks for disk usage; used only with [1m-s[0m
and per directory totals

[1m-l     [22muse a long listing format

[1m-L[22m, [1m--dereference[0m
when showing file information for a symbolic link, show informa‐
tion  for  the file the link references rather than for the link
itself

[1m-m     [22mfill width with a comma separated list of entries

[1m-n[22m, [1m--numeric-uid-gid[0m
like [1m-l[22m, but list numeric user and group IDs

[1m-N[22m, [1m--literal[0m
print entry names without quoting

[1m-o     [22mlike [1m-l[22m, but do not list group information

[1m-p[22m, [1m--indicator-style[22m=[4mslash[0m
append / indicator to directories

[1m-q[22m, [1m--hide-control-chars[0m
print ? instead of nongraphic characters

[1m--show-control-chars[0m
show nongraphic characters as-is (the default, unless program is
'ls' and output is a terminal)

[1m-Q[22m, [1m--quote-name[0m
enclose entry names in double quotes

[1m--quoting-style[22m=[4mWORD[0m
use  quoting style WORD for entry names: literal, locale, shell,
shell-always,  shell-escape,  shell-escape-always,   c,   escape
(overrides QUOTING_STYLE environment variable)

[1m-r[22m, [1m--reverse[0m
reverse order while sorting

[1m-R[22m, [1m--recursive[0m
list subdirectories recursively

[1m-s[22m, [1m--size[0m
print the allocated size of each file, in blocks

[1m-S     [22msort by file size, largest first

[1m--sort[22m=[4mWORD[0m
sort  by  WORD instead of name: none ([1m-U[22m), size ([1m-S[22m), time ([1m-t[22m),
version ([1m-v[22m), extension ([1m-X[22m)

[1m--time[22m=[4mWORD[0m
with [1m-l[22m, show time as WORD instead of default modification time:
atime  or  access  or  use  ([1m-u[22m); ctime or status ([1m-c[22m); also use
specified time as sort key if [1m--sort[22m=[4mtime[24m (newest first)

[1m--time-style[22m=[4mTIME_STYLE[0m
time/date format with [1m-l[22m; see TIME_STYLE below

[1m-t     [22msort by modification time, newest first

[1m-T[22m, [1m--tabsize[22m=[4mCOLS[0m
assume tab stops at each COLS instead of 8

[1m-u     [22mwith [1m-lt[22m: sort by, and show, access time; with [1m-l[22m:  show  access
time  and  sort  by name; otherwise: sort by access time, newest
first

[1m-U     [22mdo not sort; list entries in directory order

[1m-v     [22mnatural sort of (version) numbers within text

[1m-w[22m, [1m--width[22m=[4mCOLS[0m
set output width to COLS.  0 means no limit

[1m-x     [22mlist entries by lines instead of by columns

[1m-X     [22msort alphabetically by entry extension

[1m-Z[22m, [1m--context[0m
print any security context of each file

[1m-1     [22mlist one file per line.  Avoid '\n' with [1m-q [22mor [1m-b[0m

[1m--help [22mdisplay this help and exit

[1m--version[0m
output version information and exit

The SIZE argument is an integer and  optional  unit  (example:  10K  is
10*1024).   Units  are  K,M,G,T,P,E,Z,Y  (powers  of 1024) or KB,MB,...
(powers of 1000).

The TIME_STYLE argument can be  full-iso,  long-iso,  iso,  locale,  or
+FORMAT.   FORMAT  is  interpreted  like in date(1).  If FORMAT is FOR‐
MAT1<newline>FORMAT2, then FORMAT1 applies to non-recent files and FOR‐
MAT2  to  recent files.  TIME_STYLE prefixed with 'posix-' takes effect
only outside the POSIX locale.  Also the TIME_STYLE  environment  vari‐
able sets the default style to use.

Using  color  to distinguish file types is disabled both by default and
with [1m--color[22m=[4mnever[24m.  With [1m--color[22m=[4mauto[24m, ls emits color codes only  when
standard  output is connected to a terminal.  The LS_COLORS environment
variable can change the settings.  Use the dircolors command to set it.

[1mExit status:[0m
0      if OK,

1      if minor problems (e.g., cannot access subdirectory),

2      if serious trouble (e.g., cannot access command-line argument).

[1mAUTHOR[0m
Written by Richard M. Stallman and David MacKenzie.

[1mREPORTING BUGS[0m
Report ls translation bugs to <https://translationproject.org/team/>

GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This  is  free  software:  you  are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Full documentation at: <https://www.gnu.org/software/coreutils/ls>
or available locally via: info '(coreutils) ls invocation'

GNU coreutils 8.29               December 2017                           LS(1)


ls -F Desktop

ls: cannot access 'Desktop': No such file or directory



Your output should be a list of all the files and sub-directories on your Desktop, including the data-shell directory you downloaded at the setup for this lesson. Take a look at your Desktop to confirm that your output is accurate.

As you may now see, using a bash shell is strongly dependent on the idea that your files are organized in a hierarchical file system. Organizing things hierarchically in this way helps us keep track of our work: it’s possible to put hundreds of files in our home directory, just as it’s possible to pile hundreds of printed papers on our desk, but it’s a self-defeating strategy.

Now that we know the data-shell directory is located on our Desktop, we can do two things.

First, we can look at its contents, using the same strategy as before, passing a directory name to ls:

ls -F Desktop/data-shell

ls: cannot access 'Desktop/data-shell': No such file or directory



Second, we can actually change our location to a different directory, so we are no longer located in our home directory.

The command to change locations is cd followed by a directory name to change our working directory. cd stands for “change directory”, which is a bit misleading: the command doesn’t change the directory, it changes the shell’s idea of what directory we are in.

Let’s say we want to move to the data directory we saw above. We can use the following series of commands to get there:

cd Desktop
cd data-shell
cd data

bash: cd: Desktop: No such file or directory
bash: cd: data-shell: No such file or directory
bash: cd: data: No such file or directory



These commands will move us from our home directory onto our Desktop, then into the data-shell directory, then into the data directory. cd doesn’t print anything, but if we run pwd after it, we can see that we are now in /Users/nelle/Desktop/data-shell/data. If we run ls without arguments now, it lists the contents of /Users/nelle/Desktop/data-shell/data, because that’s where we now are:

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks/01-bash


ls -F

01-introducing-the-shell_instructor.ipynb
01-introducing-the-shell.ipynb
02-files-and-directories_instructor.ipynb
02-files-and-directories.ipynb
03-working-with-files-and-directories_instructor.ipynb
03-working-with-files-and-directories.ipynb
filesystem-challenge.svg
filesystem.svg
home-directories.svg
nano-screenshot.png
thesis/



We now know how to go down the directory tree, but how do we go up? We might try the following:

cd data-shell

bash: cd: data-shell: No such file or directory



But we get an error! Why is this?

With our methods so far, cd can only see sub-directories inside your current directory. There are different ways to see directories above your current location; we’ll start with the simplest.

There is a shortcut in the shell to move up one directory level that looks like this:

cd ..


.. is a special directory name meaning “the directory containing this one”, or more succinctly, the parent of the current directory. Sure enough, if we run pwd after running cd .., we’re back in /Users/nelle/Desktop/data-shell:

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks



The special directory .. doesn’t usually show up when we run ls. If we want to display it, we can give ls the -a flag:

ls -F -a

./			     09-time-series-data/
../			     10-units/
00-lessons_instructor.ipynb  11-tabular-data/
00-lessons.ipynb	     12-images-and-visualisation/
01-bash/		     13-images-in-astronomy/
03-fundamentals-of-python/   15-final-exercise/
04-further-python/	     environment.yml
05-writing-effective-tests/  .git
06-approximating-pi/	     .gitignore
07-collaborating-with-git/   LICENCE



-a stands for “show all”; it forces ls to show us file and directory names that begin with ., such as .. (which, if we’re in /Users/nelle, refers to the /Users directory) As you can see, it also displays another special directory that’s just called ., which means “the current working directory”. It may seem redundant to have a name for it, but we’ll see some uses for it soon.

Note that in most command line tools, multiple flags can be combined with a single - and no spaces between the flags: ls -F -a is equivalent to ls -Fa.

## Other Hidden Files

In addition to the hidden directories .. and ., you may also see a file called .bash_profile. This file usually contains shell configuration settings. You may also see other files and directories beginning with .. These are usually files and directories that are used to configure different programs on your computer. The prefix . is used to prevent these configuration files from cluttering the terminal when a standard ls command is used.

## Orthogonality

The special names . and .. don't belong to cd; they are interpreted the same way by every program. For example, if we are in /Users/nelle/data, the command ls .. will give us a listing of /Users/nelle. When the meanings of the parts are the same no matter how they're combined, programmers say they are orthogonal: Orthogonal systems tend to be easier for people to learn because there are fewer special cases and exceptions to keep track of.

These then, are the basic commands for navigating the filesystem on your computer: pwd, ls and cd. Let’s explore some variations on those commands. What happens if you type cd on its own, without giving a directory?

cd


How can you check what happened? pwd gives us the answer!

pwd

/home/stuart



It turns out that cd without an argument will return you to your home directory, which is great if you’ve gotten lost in your own filesystem.

Let’s try returning to the data directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to data in one step:

cd Desktop/data-shell/data

bash: cd: Desktop/data-shell/data: No such file or directory



Check that we’ve moved to the right place by running pwd and ls -F

If we want to move up one level from the data directory, we could use cd ... But there is another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

This allows us to move to our data-shell directory from anywhere on the filesystem (including from inside data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to data-shell.

pwd

/home/stuart


cd /Users/nelle/Desktop/data-shell

bash: cd: /Users/nelle/Desktop/data-shell: No such file or directory



Run pwd and ls -F to ensure that we’re in the directory we expect.

## Two More Shortcuts

The shell interprets the character ~ (tilde) at the start of a path to mean "the current user's home directory". For example, if Nelle's home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Last Channel button on a TV remote.

## Absolute vs Relative Paths

Starting from /Users/amanda/data/, which of the following commands could Amanda use to navigate to her home directory, which is /Users/amanda?

1. cd .
2. cd /
3. cd /home/amanda
4. cd ../..
5. cd ~
6. cd home
7. cd ~/data/..
8. cd
9. cd ..

## Solution

1. No: . stands for the current directory.
2. No: / stands for the root directory.
3. No: Amanda's home directory is /Users/amanda.
4. No: this goes up two levels, i.e. ends in /Users.
5. Yes: ~ stands for the user's home directory, in this case /Users/amanda.
6. No: this would navigate into a directory home in the current directory if it exists.
7. Yes: unnecessarily complicated, but correct.
8. Yes: shortcut to go back to the user's home directory.
9. Yes: goes up one level.

## Relative Path Resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls -F ../backup display?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original/ pnas_final/ pnas_sub/

## Solution

1. No: there is a directory backup in /Users.
2. No: this is the content of Users/thing/backup, but with .. we asked for one level further up.
3. No: see previous explanation.
4. Yes: ../backup/ refers to /Users/backup/.

## ls Reading Comprehension

Assuming a directory structure as in the above Figure (File System for Challenge Questions), if pwd displays /Users/backup, and -r tells ls to display things in reverse order, what command will display:

pnas_sub/ pnas_final/ original/

1. ls pwd
2. ls -r -F
3. ls -r -F /Users/backup
4. Either #2 or #3 above, but not #1.

## Solution

1. No: pwd is not the name of a directory.
2. Yes: ls without directory argument lists files and directories in the current directory.
3. Yes: uses the absolute path explicitly.
4. Correct: see explanations above.

### Nelle’s Pipeline: Organizing Files

Knowing just this much about files and directories, Nelle is ready to organize the files that the protein assay machine will create. First, she creates a directory called north-pacific-gyre (to remind herself where the data came from). Inside that, she creates a directory called 2012-07-03, which is the date she started processing the samples. She used to use names like conference-paper and revised-results, but she found them hard to understand after a couple of years. (The final straw was when she found herself creating a directory called revised-revised-results-3.)

## Sorting Output

Nelle names her directories "year-month-day", with leading zeroes for months and days, because the shell displays file and directory names in alphabetical order. If she used month names, December would come before July; if she didn't use leading zeroes, November ('11') would come before July ('7'). Similarly, putting the year first means that June 2012 will come before June 2013.

Each of her physical samples is labelled according to her lab’s convention with a unique ten-character ID, such as “NENE01729A”. This is what she used in her collection log to record the location, time, depth, and other characteristics of the sample, so she decides to use it as part of each data file’s name. Since the assay machine’s output is plain text, she will call her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same directory.

Now in her current directory data-shell, Nelle can see what files she has using the command:

ls north-pacific-gyre/2012-07-03/

ls: cannot access 'north-pacific-gyre/2012-07-03/': No such file or directory



This is a lot to type, but she can let the shell do most of the work through what is called tab completion. If she types:

ls nor

ls: cannot access 'nor': No such file or directory



and then presses tab (the tab key on her keyboard), the shell automatically completes the directory name for her:

ls north-pacific-gyre/

ls: cannot access 'north-pacific-gyre/': No such file or directory



If she presses tab again, Bash will add 2012-07-03/ to the command, since it’s the only possible completion. Pressing tab again does nothing, since there are 19 possibilities; pressing tab twice brings up a list of all the files, and so on. This is called tab completion, and we will see it in many other tools as we go on.

Keypoints:

• "The file system is responsible for managing information on the disk."
• "Information is stored in files, which are stored in directories (folders)."
• "Directories can also store other directories, which forms a directory tree."
• "cd path changes the current working directory."
• "ls path prints a listing of a specific file or directory; ls on its own lists the current working directory."
• "pwd prints the user's current working directory."
• "/ on its own is the root directory of the whole file system."
• "A relative path specifies a location starting from the current location."
• "An absolute path specifies a location from the root of the file system."
• "Directory names in a path are separated with / on Unix, but \\ on Windows."
• ".. means 'the directory above the current one'; . on its own means 'the current directory'."
• "Most files' names are something.extension. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file."

The material in this notebook is derived from the Software Carpentry lessons © Software Carpentry under the terms of the CC-BY 4.0 license.