Discovering the linux world through jupyter

Christine Tranchant-Dubreuil and François Sabot

The objectives

Run your own analysis using jupyter book and Linux !

After this course, you will able to :

• Know the main Linux commands
• Move into the Linux file tree : pwd, ls, cd, mkdir`
• Work with text files: head, tail, wc, grep
• Chain and combine commands
• Run programs from the command line

What is Linux ?

An operating system well known for :

• its security and stability
• its frequent updates
• its (no) fees and openSource (mostly) softwares

Created in 1991 by Linus Torvalds

Linux source code opensource and free : copy, modify, redistribute

What is Linux ?

• Robust et multi-plateform OS : computer, server, android…

• Multi-users system : Several users can work simultaneously

• Multi-tasking system (processes/programs) Every user can run several programs at the same time

How to use Linux ?

• 2 classical ways :

  Graphical User Interface
  

How to use Linux ?

• 2 classical ways :

  Graphical User Interface

  Command-Line Interface through a terminal
  

How to use Linux ?

• a new and alternative ways :

  jupyter book
  

Why using Linux ?

• Numerous fast and powerful programs

• Easy to link commands and programs (workflow)

• Numerous bioinformatics softwares available

• 90% of servers on Linux

Why using Linux ?

Need to practice!!!

Important investissments to have good results !!!

Let's go through jupyter

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

2nd command ls

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

ls

ls + option -l

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

ls -l

2nd command + argument ls

with directory path as argument

ls /home/jovyan/SV_DATA/REF

• What is a file tree for Linux?

The file tree - file system

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

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

• What is the difference between the absolute and relative path ?

What is an absolute path of a file or a directory ?

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

ABSOLUTE
Complete path of a file starting from the root directory /
starts always with /
always good wherever user is working

What is a relative path of a file or a directory ?

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

	RELATIVE
	Path related to the present working directory (where the user is working)
	Never starts with /
	Depends on where the user is working

In brief

• 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

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

Absolute Path

• Always start with / (root directory)

• Always works wherever user is working on the server or vm

• What is the absolute path of the directory script ?

Relative Path

• Path related to the present working directory

• Never starts with /

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

Relative Path

• Path related to the present working directory

• Never starts with /

• What is the relative path of the directory fasta ?

Rules for naming file and directory names

• linux is case sensitive

    Sequence.fasta    SEQUENCE.fasta   sequence.fasta

Rules for naming file and directory names

• linux is case sensitive
• Only ROMAN letters, numbers and _ -

Rules for naming file and directory names

• linux is case sensitive

• Only ROMAN letters, numbers and _ -

• No space, accent or special symbol

    & ~ # ”  ' { ( [ | ` \ ^ @ ) ] } $ * % ! / ; , ?

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.

A few Basic Commands

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

A few Basic Commands

How to get help about one command

• with the ’option --help ou -h
• with the command man

Command cd

• Move from the current directory into a new directory

cd DIRECTORY NAME (absolute or relative path)

• Move into the REF directory (absolute path)

• Move into the SV_DATA directory (absolute path)

• Move into the SHORT_READS directory (relative path)

Some Commands

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

Commands for displaying text files and searching word

command cat

• cat nom_fichier : Displays the content of a file on the screen

(Don’t use it with big files!!)

cat _PUT_THE_CORRECT_PATH_TO_ASSEMBLIES/assembly-stats.txt_

command wc

• wc -l : Displays the nomber of lines in a file

wc -l PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff

command head

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

head PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff

head -n 20 PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff

command tail

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

tail PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff