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Credits : This survival guide on Linux was created by C. Tranchant.

First steps on Linux#

Commands for moving around the file system and manipulating files/folders

Linux command syntax#

command [ -options] [ arguments ]

Your first command pwd#

pwd print the name of the current directory (the full path)

pwd
answer 
/home/toto/

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2nd command ls#

Without argument : list all the files in the current directory (by default)

ls

2nd command + option ls -l#

ls -l : list files with more information about each file (long)

ls -l

2nd command + argument#

with argument <=> directory path

ls PUT_HERE_DIRECTORY_NAME

Question

list the content of the directory REF

answer 
ls /home/joyvan/SV_DATA/REF

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obtaining help#

How to get help about one command

With the option --help ou -h

With the command man

A summary of survival commands#

command action
pwd Display the full path of the current directory
ls List all files/directories
ls -l Display all files (Long listing)

The file tree#

The file tree - file system#

Directory structure starts at the root directory called “/” (slash)

Question

list the content of the root directory

The file tree - Main directories#

Path of a file#

Path = location to a file/directory in the file system

On linux filetree, you can use absolute or relative path

Question

What is the difference between the absolute and relative path ?

In brief : absolute vs relative path#

Path = location to a file/directory in the file system

ABSOLUTE RELATIVE
Complete path of a file
starting from the root directory /		 Path related to the present working directory
(where the user is working)
starts always with / Never starts with /
always good wherever user is working Depends on where the user is working

Absolute Path#

Always start with / (root directory)

Always works wherever user is working on the server or vm

Question

What is the absolute path of the file sequence.fasta ?

answer 
ls /home/sabot/data/fasta/sequence.fasta

Question

What is the absolute path of the directory script ?

answer 
ls /home/sabot/script

Relative Path#

Path related to the present working directory

Never starts with /

Question

What is the relative path of the file sequence.fasta ?

answer 
ls fasta/sequence.fasta

Question

What is the relative path of the directory fasta ?

answer 
ls .

Rules for naming file and directory names#

  • Linux is case sensitive

  • Only ROMAN letters, numbers and _ -

  • No space, accent or special symbol

  • No need to use filename extension (.txt), just to improve readability of filenames.

Command cd#

cd as Change Directory

Move from the current directory into a new directory

cd DIRECTORY NAME (could be absolute or relative path)

Question

Move into the REF directory (absolute path)

answer 
cd /home/jovyan/SV_DATA/REF

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Question

Move into the SV_DATA directory (absolute path)

answer 
cd /home/jovyan/SV_DATA

Question

Move into the SHORT_READS directory (relative path)

answer 
cd SHORT_READS/

Some Commands#

command action
pwd Display the full path of the current directory
ls List all files/directories
cd DIR_NAME Change the working directory
rm nom_fichier Remove a directory
cp file1 file2 Make a copy of file1 and calls it file2
cp FILE_NAME DIR_NAME Copy the file FILE_NAME in the directory DIR_NAME
cp FILE DIR/NEW_FILE Mix of 2

command cat#

cat file_name Displays the content of a file on the screen

Warning

Don’t use it with big files!!

cat sequence.fasta

command wc#

wc -l : Displays the number of lines in a file

wc -l sequence.fasta

command head#

head nom_fichier : writes the first ten lines of a file to the screen

head sequence.fasta

head -n 20 sequence.fasta

command tail#

tail nom_fichier : writes the last ten lines of a file to the screen

tail sequence.fasta