{ "cells": [ { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Discovering the linux world through jupyter \n", "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "Christine Tranchant-Dubreuil and François Sabot " ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## The objectives\n", "\n", "\t Run your own analysis using jupyter book and Linux !\n", " \n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "After this course, you will able to :\n", "\n", "* Know the main Linux commands\n", "* Move into the Linux file tree : `pwd`, `ls`, `cd`, mkdir` \n", "* Work with text files: `head`, `tail`, `wc`, `grep`\n", "* Chain and combine commands\n", "* Run programs from the command line\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# What is Linux ?\n", "\n", "\n", "\n", "\n", "An operating system well known for :\n", " * its security and stability\n", " * its frequent updates\n", " * its (no) fees and openSource (mostly) softwares\n", " \n", "**Created in 1991 by Linus Torvalds**\n", "\n", "Linux source code **opensource** and **free** : copy, modify, redistribute\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# What is Linux ?\n", "\n", "\n", "\n", "* ***Robust et multi-plateform OS*** : computer, server, android…\n", "\n", "* ***Multi-users system*** : Several users can work simultaneously\n", "\n", "* ***Multi-tasking system (processes/programs)***\n", "
\n", "Every user can run several programs at the same time\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# How to use Linux ?\n", "\n", "* 2 classical ways :\n", "\n", " **Graphical User Interface** \n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# How to use Linux ?\n", "\n", "\n", "* 2 classical ways :\n", "\n", " **Graphical User Interface** \n", " \n", " **Command-Line Interface through a terminal** \n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# How to use Linux ?\n", "\n", "\n", "* a new and alternative ways :\n", "\n", " **jupyter book** \n", "\n", "\n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Why using Linux ?\n", "\n", "\n", "* Numerous fast and powerful programs\n", "\n", "* Easy to link commands and programs (workflow)\n", "\n", "* Numerous bioinformatics softwares available \n", "\n", "* 90% of servers on Linux\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Why using Linux ?\n", "\n", "Need to practice!!! \n", "\n", "**Important investissments to have good results !!!**\n", " \n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Let's go through jupyter\n", "\n", "\n", "\n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# First steps on Linux\n", "\n", "Commands for *moving around the file system* and *manipulating files/folders*\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Linux command syntax\n", "\n", "command [ -options] [ arguments ]\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Your first command _pwd_\n", "\n", "**pwd** print the name of the current directory (the full path)" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "pwd" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "fragment" } }, "source": [ "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# 2nd command _ls_\n", "\n", "* without argument : list all the files in the current directory (by default)\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "ls" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# ls + option -l\n", "\n", "ls -l : _list files with more information about each file_ (long)" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "ls -l" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# 2nd command + argument _ls_\n", "\n", "with directory path as argument" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "ls /home/jovyan/SV_DATA/REF" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ " \n", "\n", "
\n", "\n", "* What is a file tree for Linux?\n", " \n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# The file tree - file system\n", "\n", "* Directory structure starts at the root directory called “/” (slash) \n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# The file tree - Main directories\n", "\n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Path of a file\n", "\n", "* Path = location to a file/directory in the file system\n", "\n", "* On linux filetree, you can use absolute or relative path \n", "\n", " \n", "\n", "* What is the difference between the absolute and relative path ?\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# What is an absolute path of a file or a directory ?\n", "\n", "* Path = location to a file/directory in the file system\n", "\n", "| ABSOLUTE | |\n", "|:------|:------|\n", "| Complete path of a file
starting from the root directory / | |\n", "| starts always with / | |\n", "| always good wherever user is working | | \n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# What is a relative path of a file or a directory ?\n", "\n", "* Path = location to a file/directory in the file system\n", "\n", "| | RELATIVE |\n", "|:------|:------|\n", "| | Path related to the present working directory
(where the user is working) |\n", "| | Never starts with / |\n", "| | Depends on where the user is working| \n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# In brief\n", "\n", "* Path = location to a file/directory in the file system\n", "\n", "| ABSOLUTE | RELATIVE |\n", "|:------|:------|\n", "| Complete path of a file
starting from the root directory / | Path related to the present working directory
(where the user is working) |\n", "| starts always with / | Never starts with / |\n", "| always good wherever user is working | Depends on where the user is working| \n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Absolute Path \n", "\n", "* Always start with / (root directory)\n", "\n", "* Always works wherever user is working on the server or vm\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "fragment" } }, "source": [ " \n", "\n", "* What is the absolute path of the file sequence.fasta ?\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Absolute Path \n", "\n", "* Always start with / (root directory)\n", "\n", "* Always works wherever user is working on the server or vm\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "fragment" } }, "source": [ " \n", "\n", "* What is the absolute path of the directory script ?\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Relative Path \n", "\n", "* Path related to the present working directory\n", "\n", "* Never starts with /\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "fragment" } }, "source": [ " \n", "\n", "* What is the relative path of the file sequence.fasta ?\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Relative Path \n", "\n", "* Path related to the present working directory\n", "\n", "* Never starts with /\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "fragment" } }, "source": [ " \n", "\n", "* What is the relative path of the directory fasta ?\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Rules for naming file and directory names\n", "\n", "* linux is case sensitive\n", "\n", " Sequence.fasta SEQUENCE.fasta sequence.fasta" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Rules for naming file and directory names\n", "\n", "* linux is case sensitive\n", "* Only ROMAN letters, numbers and _ -" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Rules for naming file and directory names\n", "\n", "* linux is case sensitive\n", "* Only ROMAN letters, numbers and _ -\n", "* No space, accent or special symbol\n", "\n", " & ~ # ” ' { ( [ | ` \\ ^ @ ) ] } $ * % ! / ; , ?\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Rules for naming file and directory names\n", "\n", "* linux is case sensitive\n", "* Only ROMAN letters, numbers and _ -\n", "* No space, accent or special symbol\n", "* No need to use filename extension (.txt), just to improve readability of filenames. \n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# A few Basic Commands\n", "\n", "\n", "| | |\n", "|------|------|\n", "| pwd | Display the full path of the current directory|\n", "| ls | List all files/directories|\n", "| ls -l | Display all files (Long listing)|\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# A few Basic Commands\n", "\n", "How to get help about one command\n", "\n", "* with the ’option --help ou -h \n", "* with the command man " ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Command _cd_\n", "\n", " \n", "* Move from the current directory into a new directory\n", "\n", "__cd DIRECTORY NAME (absolute or relative path)__" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ " \n", "\n", "* Move into the REF directory (absolute path)\n", " \n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ " \n", "\n", "* Move into the SV_DATA directory (absolute path)\n", " \n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ " \n", "\n", "* Move into the SHORT_READS directory (relative path)\n", " \n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Some Commands\n", "\n", "\n", "| | |\n", "|:------|:------|\n", "| pwd | Display the full path of the current directory|\n", "| ls | List all files/directories|\n", "| cd DIR_NAME| Change the working directory|\n", "| rm nom_fichier | Remove a directory |\n", "| cp file1 file2 | Make a copy of file1 and calls it file2 |\n", "| cp FILE_NAME DIR_NAME | Copy the file FILE_NAME in the directory DIR_NAME |\n", "| cp FILE DIR/NEW_FILE | Mix of 2 |\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Commands for displaying text files and searching word" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# command cat\n", "\n", "* `cat nom_fichier` : Displays the content of a file on the screen\n", "\n", "(Don’t use it with big files!!)\n", "\n", "\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "cat _PUT_THE_CORRECT_PATH_TO_ASSEMBLIES/assembly-stats.txt_" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# command wc\n", "\n", "* `wc -l` : Displays the nomber of lines in a file\n", "\n", "\n", "\n", "\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "wc -l PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# command head\n", "\n", "* `head nom_fichier` : writes the first ten lines of a file to the screen" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "head PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "scrolled": true, "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "head -n 20 PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# command tail\n", "\n", "* `tail nom_fichier` : writes the last ten lines of a file to the screen\n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "slideshow": { "slide_type": "fragment" } }, "outputs": [], "source": [ "tail PUT_THE_CORRECT_PATH_TO_REF/GCA_002220235.1_ASM222023v1_genomic.gff" ] } ], "metadata": { "celltoolbar": "Diaporama", "kernelspec": { "display_name": "Bash", "language": "bash", "name": "bash" }, "language_info": { "codemirror_mode": "shell", "file_extension": ".sh", "mimetype": "text/x-sh", "name": "bash" }, "rise": { "enable_chalkboard": true } }, "nbformat": 4, "nbformat_minor": 4 }