Use a language it understands, e.g. BASH (Bourne Again SHell)
1:
the BASH language is one of many extremely
similar Shell dialects (bsh, ksh,
csh, zsh, …)
BASH is based on a set of modular commands,
which perform specific tasks
Commands are written just after the prompt.
Here, the $ character symbolizes that the computer is
waiting/ready for your commands.
__
(1) A pun on the first Shell language written by Stephen Bourne
himself (bsh)
Prototype of a command
a command performs a task
(sorting, selecting, opening, aligning reads, etc.)
generally speaking, a terminal instruction always begins with the
name of a command
it has a certain number of arguments*, which may be
optional, and which can modify its mode of operation
# below, the format [xxx] indicates that xxx is an optional elementcommand_name [argument_name [argument_value]] [file]
argument names are not standardized
arguments may or may not take values
arguments may have short and/or long forms
/!\ spaces between the command and its arguments are seen as
separators
*there’s no standard term for ‘arguments’, you may also
come accross the terms ‘flags’ or ‘options’
Example using the
cal command (part 1)
cal (short for calendar) is a handy command to view a
certain date, month or year:
⮕ without arguments
c.toffano-nioche@SSFA-18:$ calAvril 2024 di lu ma me je ve sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
⮕ with a single argument
with no value
cal -3 displays 3 months, centered on the current
month:
c.toffano-nioche@SSFA-18:$ cal -3Mars 2024 Avril 2024 Mai 2024 di lu ma me je ve sa di lu ma me je ve sa di lu ma me je ve sa 1 2 1 2 3 4 5 6 1 2 3 4 3 4 5 6 7 8 9 7 8 9 10 11 12 13 5 6 7 8 9 10 11 10 11 12 13 14 15 16 14 15 16 17 18 19 20 12 13 14 15 16 17 18 17 18 19 20 21 22 23 21 22 23 24 25 26 27 19 20 21 22 23 24 25 24 25 26 27 28 29 30 28 29 30 26 27 28 29 30 31 31
Example using the
cal command (part 2)
⮕ with a single
argument which requires a value
c.toffano-nioche@SSFA-18:$ cal -m mayMai 2024 di lu ma me je ve sa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
⮕ short vs long forms of an
argument
often, arguments have short & long forms (more explicit/readable
but longer to type…)
long forms are generally preceded by two dashes
e.g. instead of cal -3, we can use
cal --three
c.toffano-nioche@SSFA-18:$ cal --threeMars 2024 Avril 2024 Mai 2024 di lu ma me je ve sa di lu ma me je ve sa di lu ma me je ve sa 1 2 1 2 3 4 5 6 1 2 3 4 3 4 5 6 7 8 9 7 8 9 10 11 12 13 5 6 7 8 9 10 11 10 11 12 13 14 15 16 14 15 16 17 18 19 20 12 13 14 15 16 17 18 17 18 19 20 21 22 23 21 22 23 24 25 26 27 19 20 21 22 23 24 25 24 25 26 27 28 29 30 28 29 30 26 27 28 29 30 31 31
How to get help?
Call the police, call your colleagues, search the Internet… or use
the man command (manual)
c.toffano-nioche@SSFA-18:~$ man cal
CAL(1) User Commands CAL(1)
NAME
cal - display a calendar
SYNOPSIS
cal [options] [[[day] month] year]
DESCRIPTION
cal displays a simple calendar. If no arguments are specified, the current
month is displayed.
OPTIONS
-1, --one
Display single month output. (This is the default.)
-3, --three
Display prev/current/next month output.
...
SYNOPSIS explains how to write the command line;
optional elements are written between [..] DESCRIPTION describes the result of the command OPTIONS list the available arguments, with their short and
long forms
Shortcuts for the
man interface:
navigate with your keyboard arrows (↑ & ↓)
/color: to search for the term color
n: (next) to search for the next occurrence of the term
searched for
p: (previous) to search for the previous occurrence of
the term searched for
q: to quit help
__
*Custom programmes/commands or scripts often have the
-h or --help arguments to print help messages
on how to use them.
Focus on the ls command and its arguments
The ls command lists
directory contents and can take a number of arguments.
Among the main arguments:
-l (long/lots) gives
a lot of information about files
-a (--all) shows all files, including
hidden ones
-t (time) sorts by modification date
-h (--human-readable) displays file sizes
in readable units
-r (--reverse) reverses sort order
Notes:
names of hidden files & folders begin with a dot (e.g..git)
. and .. directories are special (detailed
later)
pay attention to the spaces between the command and its arguments.
The ls-l command does not exist!
Focus on the ls command and its arguments (page 2)
⮕ Arguments can be
combined: ls -l --all
c.toffano-nioche@SSFA-18:~/formation_bash0$ ls -l --all
total 56
drwxr-xr-x 4 c.toffano-nioche tous 4096 avril 18 11:18 .
drwxr-xr-x 4 c.toffano-nioche tous 4096 avril 17 18:51 ..
-rw-r--r-- 1 c.toffano-nioche tous 587 avril 16 16:06 bash0_chatTerm.md
-rw-r--r-- 1 c.toffano-nioche tous 1131 avril 17 19:02 bash0_FindingHelp.md
-rw-r--r-- 1 c.toffano-nioche tous 833 avril 18 11:18 bash0_zoomLS.md
drwxr-xr-x 8 c.toffano-nioche tous 4096 avril 18 11:08 .git
drwxr-xr-x 2 c.toffano-nioche tous 4096 avril 16 15:14 images
⮕ Arguments
can be merged (in short format): ls -lahtr
for a complete (-a) and detailed view (-l),
sizes in KB,MB,GB,TB… i.e. human readable (-h),
sorted by date/time (-t) from oldest to most recent
(-r):
c.toffano-nioche@SSFA-18:~/formation_bash0$ ls -lahtr
total 56K
drwxr-xr-x 2 c.toffano-nioche tous 4.0K avril 16 15:14 images
-rw-r--r-- 1 c.toffano-nioche tous 587 avril 16 16:06 bash0_chatTerm.md
drwxr-xr-x 4 c.toffano-nioche tous 4.0K avril 17 18:51 ..
-rw-r--r-- 1 c.toffano-nioche tous 1.2K avril 17 19:02 bash0_FindingHelp.md
drwxr-xr-x 8 c.toffano-nioche tous 4.0K avril 18 11:08 .git
drwxr-xr-x 4 c.toffano-nioche tous 4.0K avril 18 11:18 .
-rw-r--r-- 1 c.toffano-nioche tous 833 avril 18 11:18 bash0_zoomLS.md
Filesystems are like trees
General information
The filesystem can be compared to a tree where leaves are
directories and files. We can go throught it by following the
branches.
The tree is anchored by the root: the / directory
General information (part 2)
When we go up in the tree (=down in the hierarchy) by following the
branches, we can see that the / (root) contains multiple
directories (e.g. shared)
General information (part 3)
The shared directory contains
bank
General information (part 4)
The bank directory contains
homo_sapiens
General information (part 5)
Thus, the pathway to go in the homo_sapiens directory
from the root is : /shared/bank/homo_sapiens
Navigate in the file tree
Our goal is to get to the homo_sapiens directory. For
this, we are going to use the pwd (=print work directory)
and cd (=change directory) commands. We have two
choices:
Specify the path from the root directory (symbolized by
/)
Specify the path from the current directory (symbolized by
.)
ant_monkey.png
1.
Specify the path from the root directory (/) : absolute
path
# To change, all the directories names have to be separate by /cd /shared/bank/homo_sapienspwd
2.
Specify the path from the current directory: relative path
The current directory is the directory where the user is
working
The path is relative to the current directory (.)
To go in the parent directory : cd .. or grandparent
directory : cd ../..
# To stay in the same directorycd . # same as cd ./# If the working directory is star-2.7.5a, you stay herepwd# To go up from 2 directories cd ../.. # same as cd ../../# To check the pathpwd
Navigate in the file tree
Take home message
Relative and absolute paths give the same result. If the working
directory is shared and we have to access
homo_sapiens:
Absolute path (/!\ absolute paths always start with the root
/)
It’s the user’s directory & it stores all of the user’s
documents
It’s symbolized by ~ (tilde)*
Most of the time it’s /home/userName (but it may vary
according to the infrastructure you’re on e.g. on the IFB cluster, it’s:
/shared/home/userName)
# absolute pathcd /home/userName# short way for the same resultcd ~# orcd
__
*~ for Mac users: option +
N or Alt + N
Autocompletion (<TAB><TAB>) - your new best friend!
If you want to shine in society or with your family by giving the
impression of typing quickly, use auto-completion!
More seriously:
it’s essential for typing a path without making mistakes
it also saves time because you won’t need to type every single
letter
E.g. try moving into the directory: /usr/local/bin using
<TAB><TAB>
Where can I find the tab
key?
Rest assured, you haven’t heard the last of …
How to create, copy, remove files or directories
It’s important to organise files and directories to easily find data.
4 commands are useful:
mkdir (make directories) : to create a directory
# read the documentationman mkdir# create a directory named my_new_dirmkdir my_new_dir# check if the directory was createdls
cp (copy) : to copy files and directories (/!\ to copy
a directory, you need to add an option)
# read the documentationman cp# create a copy of a filecp gameshell.sh copy_gameshell.sh# create a copy of a directorycp--recursive dir0/ dir1/
How to create, copy, remove files or directories
mv (move) : to move a file to an other directory or
rename it
# read the documentationman mv# rename a filemv my_file_with_a_long_useless_name_i_want_to_change.txt my_file.txt# put my_file.txt in the directory called my_dirmv my_file.txt my_dir/
rm (remove) : to remove files or directories.
Warning: it’s easy to remove more files/directories
than planned. To be sure, you can run the ls command before
to check if it’s what you want.
# read the documentationman rm# remove a filerm my_file_with_a_long_useless_name_i_want_to_change.txt
Know your rights!
Sometimes an error message may appear saying that you are “not
authorised” to perform an action…
In Linux, your rights are dictated by three letters r,
w and x:
r: read, right to read the file and open
it
w: write, right to write and modify a
file
x: execute, right to execute the file (a
script, for example)
How do I know the rights of
a file?
Remember ls -l? => ls to list
the files of a folder, -l argument to get more information
on the files
c.toffano-nioche@SSFA-18:~/formation_bash0$ ls -l
total 56
-rw-r--r-- 1 c.toffano-nioche tous 587 avril 16 16:06 bash0_chatTerm.md
-rw-r--r-- 1 c.toffano-nioche tous 1131 avril 17 19:02 bash0_FindingHelp.md
-rw-r--r-- 1 c.toffano-nioche tous 833 avril 18 11:18 bash0_zoomLS.md
drwxr-xr-x 2 c.toffano-nioche tous 4096 avril 16 15:14 images
When you type the ls -l command, you may notice that
some lines start with a d (=directory) and other with a
- (=file).
Note also the fact that rwx may or may not be repeated
three times. The first triplet corresponds to the rights held by the
owner of the file, the second corresponds to the rights allocated to
users in the same group as the owner of the file and the last
corresponds to the rights of all other users.
Accessing file contents
We’re often interested in the content of files:
reading files, counting the number of lines, extracting
a part (lines, columns), sorting lines, etc. Warning:
some commands cannot access compressed files.
Counting the number of lines
wc (word count): count the number of lines, words and
bytes of file(s)
# -l : count the number of lines in my_file.txtwc-l my_file.txt
Read a file
With less or more you can read a file line
by line (pager tool)
With head or tail you can visualize the
first n lines or the last n lines of a file
With cat you print the full contents of the file
To navigate in the file when you are using less, it’s
the same as the man command:
commands
results
↑ or ↓
Go up or down in the file
> or <
Go to the first or last line
/chr
Then press enter to find the word
chr
n or p
find the next or
previous word chr
q
quit
# read a file # -N : display the line number# -S : don't wrap lines even if they are longer than the screen (arrows to navigate)less-S-N my_file.txt
# print the first five lineshead-n 5 my_file.txt# print the last eleven linestail-n 11 my_file.txt
Select/remove a column in a
file
If you have a tabular file format (e.g. .csv,
.tsv, …) as below:
# file with chromosome, start, stop, name, score, strandchr1 7517 7517 NM_023732__Abcb6 . -chr10 1826 1826 NM_019487__Hebp2 . -chrX 1494 1494 NONE . -chrY 3470 3470 NA . +chr11 3054 3054 NA . -chr2 1929 1929 SITE . +
cut : removes columns from each line of files
E.g. if you want to select the name and the score columns of the file
above:
# keeped the column 1 to 3 and 6cut-f 1-3,6 myf.tsv
Some commands work on the basis of data either typed in by the user
or written in a file. It is referred to as the standard command input
stream or stdin.
Similarly, some commands provide data either displayed on screen
(e.g. the ls command) or in a file. It is referred
to as the standard command output stream or stdout.
There is a 3rd standard stream, which is the standard error stream or
stderr. Under Unix, a command that ends without an
error returns “0”, otherwise, it returns a number indicating the error
code, or an explanatory sentence. By default, the error stream is also
displayed on the screen (like the output stream).
Standard streams (arrows)
Stream redirections
When the result of a command is of interest to a subsequent
question/command, it can be transformed into a file rather than
displayed on the screen, so that the next command can read this file as
input data.
This is known as stream redirection.
E.g. below, the output file of command 1 becomes the input file of
command 2, thanks to the pipe redirection operator
indicated in red (it will be the | character in the command
line*):
redirection with pipe
Some other redirection operators:
> myfile.txt: stores the stdout stream by creating
(or overwriting) the myfile.txt file
>> myfile.txt: stores the stdout stream by adding
lines to the myfile.txt file
*|: Shift+\ on Mac
keyboards, AltGr+6 on Windows
Redirection examples
Example 1 - Count the
number of files
For example, to count the number of files (assuming the filenames all
have an extension) you can use the ls command followed by
the wc command:
ls*.*|wc-l
There’s no limit (apart from human understanding) to the number of
pipe redirections you can associate.
Example 2 - Count
number of files per user
Here is how to count the number of files created by each user in a
shared project: from the list of items (with ls), you can
extract (with cut) the user column (that starts at around
the 14th character), sort them (with sort) and then count
them with the uniq command and its -c option
(uniq lists single lines):
ls-lah*.*|cut-c 14-20 |sort|uniq-c
Example 3 - File inventory
It is possible to create a new file (named
my_txt_files.txt) containing a list of all files with a
special filter, for example, the extension .txt :
ls*.txt > my_txt_files.txt
Best practices
File naming!
Avoid spaces (it’s possible but it’s encouraged to use
“_” instead)
Keep concise (<30 characters if possible)
Use ISO 8601 formatted dates (YYYYMMDD or YYYY-MM-DD)
Avoid special characters, such as: é è ç ~ ! @ # $ % ^ & * ( ) ;
: < > ? . , { } ’ ” |
Example dealing
with file names with spaces
emiliedrouineau@is152868-2:~$ ls'file name.txt'emiliedrouineau@is152868-2:~$ cat file name.txtcat: file: No such file or directorycat: name.txt: No such file or directory
The terminal raised a cat error because it didn’t
understand the fact that “file name.txt” was a unique argument. Spaces
are commonly argument separators.
Thus, it reads your input as 2 separate files: file and
name.txt, which don’t exist.
It’s possible to use
spaces by escaping the character with a backslash
(file\ name.txt) or using quotes
("file name.txt") but it’s messy and can be a source of
future errors.
Warning with Windows/MacOS
files
Watch out for hidden characters when you edit files with Windows or
MacOS. Linux can be picky…
For example, although my script looks ok, I get an error when I run
it:
# run the script on linuxemiliedrouineau@is152868-2:~$ ./my_script_windows.shbash: ./my_script_windows.sh: /bin/bash^M: bad interpreter: No such file or directory
What is /bin/bash^M? I don’t see it in my file??!
The -A option of cat will help you see all
invisible characters:
emiliedrouineau@is152868-2:~$ cat -A ./my_script_windows.sh#!/bin/bash^M$# revomed score column from my file^M$cut-f 1-3,6 exoBed.bed > filter_exoBed.bed^M$# sorted file by chromosome name and start coordinates^M$sort-k1,1V-k2,2n filter_exoBed.bed > sort_filter_exoBed.bed^M$
Here, the end of line is not correctly encoded for linux
(^M).
/!\ No Excel or Word formats!!!!!!! Stick to simple text
formats
/!\ Avoid copy-pasting code from the web (hidden characters =
danger)
Conclusion
Now you know:
how to navigate the file system in the unix world
several commands to access file contents
that a succession of bash commands can be used to compose more
complex tasks
It’s a good start.
But there’s more to the Unix world than that!
