{"id":486,"date":"2020-11-03T12:22:20","date_gmt":"2020-11-03T11:22:20","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=486"},"modified":"2022-04-06T14:50:44","modified_gmt":"2022-04-06T12:50:44","slug":"linux-tutorial","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/linux-tutorial\/","title":{"rendered":"Tutorials &#8211; Linux tutorial"},"content":{"rendered":"<h2>Linux tutorial<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Linux Command-Line Cheat Sheet<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">christine Tranchant-Dubreuil (christine.tranchant@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">26\/02\/2018<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">20\/10\/2018<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Summary<\/h3>\n<p><!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 --><\/p>\n<ul>\n<li>\n<p><a href=\"#filesystem\">Moving around the Filesystem  and manipulating files\/folders<\/a><\/p>\n<ul>\n<li><a href=\"#pwd\">Printing the full path of the current directory <code>pwd<\/code><\/a><\/li>\n<li><a href=\"#ls\">Listing files in a directory  <code>ls<\/code><\/a><\/li>\n<li><a href=\"#cd\">Moving in the file tree  <code>cd<\/code><\/a><\/li>\n<li><a href=\"#mkdir\">Making directories <code>mkdir directory_name<\/code><\/a><\/li>\n<li><a href=\"#cp\">Copying files <code>cp<\/code><\/a><\/li>\n<li><a href=\"#mv\">Moving files <code>mv<\/code><\/a><\/li>\n<li><a href=\"#rm\">Removing files and directories using <code>rm<\/code>and <code>rmdir<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#display\">Displaying the contents of a file on the screen<\/a><\/p>\n<ul>\n<li><a href=\"#clear\">clear (clear screen) <code>clear<\/code><\/a><\/li>\n<li><a href=\"#cat\">Display the content of file using <code>cat<\/code><\/a><\/li>\n<li><a href=\"#less\">Display the content of file using <code>less<\/code><\/a><\/li>\n<li><a href=\"#head\">Display the begin of a file using <code>head<\/code><\/a><\/li>\n<li><a href=\"#tail\">Display the end of a file using <code>tail<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#searching\">Searching the contents of a file<\/a><\/p>\n<ul>\n<li><a href=\"#grep\">Searching word in a file using <code>grep<\/code><\/a><\/li>\n<li><a href=\"#wc\">Count for word, line count in a file using <code>wc<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#tips\">TIPS<\/a>:<\/p>\n<ul>\n<li><a href=\"#tar\">Creating and extracting a tar gz archive using <code>tar<\/code><\/a><\/li>\n<li><a href=\"#gzip\">Compressing and extracting files using <code>gzip<\/code><\/a><\/li>\n<li><a href=\"#du\">Knowing how much space a file or directory is using on a disk with <code>du<\/code><\/a><\/li>\n<li><a href=\"#ln\">Creating a file shortcut\/ a symbolic link with <code>ln -s<\/code><\/a><\/li>\n<li><a href=\"#wget\">Downloading a file over HTTP with <code>wget<\/code><\/a><\/li>\n<li><a href=\"#find\">Find files by name or extension<\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#license\">License<\/a> <\/p>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"filesystem\"><\/a><\/p>\n<h3>Moving around the Filesystem  and manipulating files\/folders<\/h3>\n<p><a name=\"pwd\"><\/a><\/p>\n<h5>Printing the name\/full path of the current directory <code>pwd<\/code><\/h5>\n<pre><code>[tranchant@master0 ~]$ pwd\n\/home\/tranchant<\/code><\/pre>\n<p><a name=\"ls\"><\/a><\/p>\n<h5>Listing files in a directory <code>ls<\/code><\/h5>\n<p><code>ls<\/code>: list all files in the current directory<\/p>\n<pre><code>[tranchant@master0 ~]$ ls \nAIRAIN\nAll-EST-coffea.fasta\nall-gene.gff3.100000.gene-density\nall_no_TE.gff3\nall_no_TE.gff3.100000.gene-density\nall_no_TE.gff3.10000.gene-density\nAll-SNP.vcf.density100000.snpden\nblast_batch.pl\nblast.sh\ncircos\nDEDUP2-1\nDEDUP2-all\nDesktop\nFASTA-TRINITY\nfastq-stat.txt\nGBS<\/code><\/pre>\n<h6>Listing files in a directory gived as argument <code>ls directory_name<\/code><\/h6>\n<pre><code>[tranchant@master0 ~]$ ls \/home \nabate\nabdelrah\nadam\nadeoti\nadereeper\nadmin\nagrondi\naichatou<\/code><\/pre>\n<h5><code>ls -l<\/code> : Display the long format listing of all files in the current directory<\/h5>\n<pre><code>[tranchant@master0 ~]$ ls -l\ntotal 148272\ndrwxr-xr-x 10 tranchant ggr      4096 13 mars   2017 AIRAIN\n-rwxr-xr-x  1 tranchant ggr  51128305 11 sept. 14:16 All-EST-coffea.fasta\n-rw-r--r--  1 tranchant ggr     95117 24 f\u00e9vr.  2017 all-gene.gff3.100000.gene-density\n-rwxr-xr-x  1 tranchant ggr  64221458 24 f\u00e9vr.  2017 all_no_TE.gff3\n-rw-r--r--  1 tranchant ggr     93796 24 f\u00e9vr.  2017 all_no_TE.gff3.100000.gene-density\n-rw-r--r--  1 tranchant ggr    889389 24 f\u00e9vr.  2017 all_no_TE.gff3.10000.gene-density\n-rwxr-xr-x  1 tranchant root    90498  5 d\u00e9c.  07:21 All-SNP.vcf.density100000.snpden\n-rwxr-xr-x  1 tranchant ggr     10366 29 mars   2017 blast_batch.pl\n-rwxr-xr-x  1 tranchant ggr       878 29 mars   2017 blast.sh\ndrwxr-xr-x  3 tranchant ggr      4096 19 janv. 15:02 circos\ndrwxr-sr-x  2 tranchant ggr      4096  8 juin   2017 DEDUP2-1\ndrwxr-sr-x  2 tranchant ggr      4096  8 juin   2017 DEDUP2-all\ndrwxr-xr-x  4 root      root     4096  9 juil.  2015 Desktop\ndrwxr-sr-x  2 tranchant ggr      8192  8 juin   2017 FASTA-TRINITY\n-rw-r--r--  1 tranchant ggr      1056 30 nov.  15:31 fastq-stat.txt\ndrwxr-xr-x  2 tranchant ggr        48 10 ao\u00fbt   2016 GBS<\/code><\/pre>\n<h5><code>ls -a<\/code> : Display all the files and directories (even hidden files)<\/h5>\n<pre><code>[tranchant@master0 ~]$ ls -a\n.                                                localConfig.pm\n..                                               .localConfig.pm.swp\nAIRAIN                                           localConfig-USR.pm\nAll-EST-coffea.fasta                             LOG\nall-gene.gff3.100000.gene-density                .ls_couleur\nall_no_TE.gff3                                   .Mathematica\nall_no_TE.gff3.100000.gene-density               .matplotlib\nall_no_TE.gff3.10000.gene-density                .Megan.def\nAll-SNP.vcf.density100000.snpden                 Microsatellite_markers\n.apollo                                          moduleLoad\n.bash_history                                    .mozilla\n.bash_logout                                     .oracle_jre_usage\n.bash_profile                                    out.sites.pi\n.bashrc                                          out.windowed.pi\nblast_batch.pl                                   parse-go.pl\nblast.sh                                         password.txt\n.cache                                           path-new.txt\ncircos                                           path.sh\n.config                                          PATH.sh\n.cpan                                            path.txt\nData-TP                                          PERL\n.dbus                                            perl5<\/code><\/pre>\n<hr \/>\n<p><a name=\"cd\"><\/a><\/p>\n<h5>Moving in the file tree  <code>cd<\/code><\/h5>\n<p><code>cd DIRECTORY_NAME<\/code> :  change the current working directory to 'directory'<br \/>\n<em>change directory<\/em><\/p>\n<pre><code>[tranchant@master0 ~]$ cd FASTQ<\/code><\/pre>\n<hr \/>\n<p><a name=\"mkdir\"><\/a><\/p>\n<h5>Making directories <code>mkdir directory_name<\/code><\/h5>\n<p><code>mkdir directory_name<\/code>: make a directory in your current working directory type<br \/>\n<em>make directory<\/em><\/p>\n<pre><code>[tranchant@master0 ~]$ mkdir results<\/code><\/pre>\n<hr \/>\n<p><a name=\"cp\"><\/a><\/p>\n<h5>Copying files <code>cp<\/code><\/h5>\n<p><em>copy<\/em><\/p>\n<ul>\n<li>\n<p><code>cp file1 file2<\/code>:  makes a copy of file1 and calls it file2<\/p>\n<\/li>\n<li>\n<p><code>cp file_name directory_name<\/code>: copy the file  _file<em>name<\/em>  to the directory _directory_name', keeping the same name.<\/p>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"mv\"><\/a><\/p>\n<h5>Moving files <code>mv<\/code><\/h5>\n<p><em>move<\/em><\/p>\n<ul>\n<li><code>mv file1 file2<\/code> :  moves (or renames) file1 to file2. It is used to rename a file, by moving the file to the same directory, but giving it a different name.<\/li>\n<li><code>mv file_na me directory<\/code> : To move the file _file<em>name<\/em> from one directory to another (here _directory<em>name<\/em>). This has the effect of moving rather than copying the file, so you end up with only one file rather than two.<\/li>\n<\/ul>\n<blockquote>\n<h2>Be careful : use preferentially cp command rather than mv command to move big files<\/h2>\n<\/blockquote>\n<p><a name=\"rm\"><\/a><\/p>\n<h5>Removing files and directories using <code>rm<\/code>and <code>rmdir<\/code><\/h5>\n<p><em>remove<\/em><\/p>\n<p><code>rm file_name<\/code>: delete (remove) a file (here _file<em>name<\/em>)<br \/>\nTo delete (remove) a file, use the rm command. As an example, we are going to create a copy of the science.txt file then delete it.<\/p>\n<p><code>rmdir directory_name<\/code> : remove a directory (make sure it is empty first because linux will not let remove a non-empty directory).<\/p>\n<hr \/>\n<p><a name=\"display\"><\/a><\/p>\n<h3>Displaying the contents of a file on the screen<\/h3>\n<p><a name=\"clear\"><\/a><\/p>\n<h5>clear (clear screen) <code>clear<\/code><\/h5>\n<p><code>clear<\/code> : clears the terminal. Before displaying files, it's possible to clear the terminal window with this command.<\/p>\n<hr \/>\n<p><a name=\"cat\"><\/a><\/p>\n<h5>Display the content of file using <code>cat<\/code><\/h5>\n<p><code>cat file1<\/code> : displays the contents of a file on the screen<br \/>\n<em>concatenate<\/em><\/p>\n<p><code>cat file1 file2<\/code><\/p>\n<p><code>cat *.fasta<\/code><\/p>\n<hr \/>\n<p><a name=\"less\"><\/a><\/p>\n<h5>Display the content of file using <code>less<\/code><\/h5>\n<p><code>less file_name<\/code> : writes the contents of a file onto the screen a page at a time. Less is used in preference to cat for long files.<\/p>\n<ul>\n<li>Press the [space-bar] if you want to see another page<\/li>\n<li>Type [q] if you want to quit reading. <\/li>\n<li>\n<p>still in less, type a forward slash [\/] followed by the word to search<\/p>\n<hr \/>\n<\/li>\n<\/ul>\n<p><a name=\"head\"><\/a><\/p>\n<h5>Display the begin of a file using <code>head<\/code><\/h5>\n<p><code>head file_name<\/code> : writes the first ten lines of a file to the screen.<\/p>\n<pre><code>[tranchant@master0 ~]$ head \nhead -n 5<\/code><\/pre>\n<hr \/>\n<p><a name=\"tail\"><\/a><\/p>\n<h5>Display the end of a file using <code>head<\/code><\/h5>\n<p><code>tail file_name<\/code> : writes the last ten lines of a file to the screen.<\/p>\n<pre><code>[tranchant@master0 ~]$ tail\ntail -n 5<\/code><\/pre>\n<hr \/>\n<p><a name=\"searching\"><\/a><\/p>\n<h3>Searching the contents of a file<\/h3>\n<p><a name=\"grep\"><\/a><\/p>\n<h5>Searching word in a file using <code>grep<\/code><\/h5>\n<p><code>grep motif file_name<\/code> : searches files for specified words or patterns. First clear the screen, then type<\/p>\n<blockquote>\n<p>To search for a phrase or pattern, you must enclose it in single quotes (the apostrophe symbol). For example to search for spinning top, type<\/p>\n<\/blockquote>\n<pre><code># printed out each line containg the word science.\n\n# The grep command is case sensitive; it distinguishes between Science and science.\n\n#To ignore upper\/lower case distinctions, use the -i option, i.e. type\n[tranchant@master0 ~]$grep -i science science.txt\n\n#\n[tranchant@master0 ~]$grep -i &#039;spinning top&#039; science.txt\n<\/code><\/pre>\n<blockquote>\n<p>Some of the other options of grep are:<\/p>\n<p>-v display those lines that do NOT match<br \/>\n-n precede each matching line with the line number<br \/>\n-c print only the total count of matched lines <\/p>\n<p>Try some of them and see the different results. Don't forget, you can use more than one option at a time. For example, the number of lines without the words science or Science is grep -ivc science science.txt<\/p>\n<\/blockquote>\n<hr \/>\n<p><a name=\"wc\"><\/a><\/p>\n<h5>Count for word, line count in a file using <code>wc<\/code><\/h5>\n<p><code>MARKDOWN_HASH8399d88e3293cc89cacc1d735af12810MARKDOWN<em>HASH<\/code>:  short for word count<br \/>\n<\/em>(word count)_<\/p>\n<hr \/>\n<p><a name=\"tar\"><\/a><\/p>\n<h5>Creating and extracting a tar gz archive using <code>tar<\/code><\/h5>\n<ul>\n<li>To create a tar.gz archive from a given folder <\/li>\n<\/ul>\n<pre><code># compress the contents of source-folder-name to a tar.gz archive named tar-archive-name.tar.gz\n[tranchant@master0 ~]$tar -zcvf tar-archive-name.tar.gz source-folder-name <\/code><\/pre>\n<ul>\n<li>To extract a tar.gz compressed archive\n<pre><code># extract the archive to the folder tar-archive-name. \ntar -zxvf tar-archive-name.tar.gz <\/code><\/pre>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"tips\"><\/a><\/p>\n<p><a name=\"gzip\"><\/a><\/p>\n<h5>Compressing and extracting files using <code>gzip<\/code><\/h5>\n<ul>\n<li><code>gzip {filename}<\/code><\/li>\n<li><code>gzip -d {.gz file}<\/code><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"du\"><\/a><\/p>\n<h5>Knowing how much space a file or directory is using on a disk with <code>du<\/code><\/h5>\n<p><code>du [options] [file or dir]<\/code><\/p>\n<p>If you use it with no arguments you will the usage of all files and directories (recursively) of the working directory.<\/p>\n<blockquote>\n<p>-h : Shows the in human readable format<br \/>\n-s : Sumarize, so it displays the total of each subdirectory and not for its contents<\/p>\n<\/blockquote>\n<hr \/>\n<p><a name=\"ln\"><\/a><\/p>\n<h5>Creating a file shortcut\/ a symbolic link with <code>ln -s<\/code><\/h5>\n<p>A symbolic link, also termed a soft link, is a special kind of file that points to another file, much like a shortcut in Windows or a Macintosh alias.<\/p>\n<p><code>ln -s source_file myfile<\/code><\/p>\n<ul>\n<li>_source<em>file<\/em> corresponds to the name of the existing file for which the symbolic link  is created (this file can be any existing file or directory across the file systems). <\/li>\n<li><em>myfile<\/em> is the name of the symbolic link. <\/li>\n<\/ul>\n<p>Note :<\/p>\n<ul>\n<li>If the source file is deleted or moved it to a different location, the symbolic file will not function properly and should be either deleted or moved it.<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"wget\"><\/a><\/p>\n<h5>Downloading a file over HTTP with <code>wget<\/code><\/h5>\n<p><code>wget http:\/\/website.com\/files\/file.zip<\/code> : downloads the file <code>http:\/\/website.com\/files\/file.zip<\/code> into the working directory.<\/p>\n<hr \/>\n<p><a name=\"find\"><\/a><\/p>\n<h5>Find files by name or extension with <code>find<\/code><\/h5>\n<p><code>find options path motif_file<\/code><\/p>\n<ul>\n<li>the <code>path<\/code> argument defines the top level directory where find begins filtering<\/li>\n<li>the <code>motif_file<\/code> argument gives the motif searched in the filename within the directory (and all sub-directories)<\/li>\n<\/ul>\n<p>The following example search for <em>k64<\/em> files in the current directory and all sub-directories:<\/p>\n<pre><code>[durreuic@cobalt172 ~]$find . -name &quot;*k64*&quot; \n.\/mappingGlabv2\/fastqPairedUnmappedBartiivsOmap\/TEST\/k64ctg-TOGGLEmappingRE\n.\/mappingGlabv2\/fastqPairedUnmappedBartiivsOmap\/TEST\/k64`<\/code><\/pre>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Linux tutorial Description Linux Command-Line Cheat Sheet Authors christine Tranchant-Dubreuil (christine.tranchant@ird.fr) Creation Date 26\/02\/2018 Last Modified Date 20\/10\/2018 Summary Moving&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/linux-tutorial\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":1325,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-486","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Tutorials - Linux tutorial - itrop<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/linux-tutorial\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorials - Linux tutorial - itrop\" \/>\n<meta property=\"og:description\" content=\"Linux tutorial Description Linux Command-Line Cheat Sheet Authors christine Tranchant-Dubreuil (christine.tranchant@ird.fr) Creation Date 26\/02\/2018 Last Modified Date 20\/10\/2018 Summary Moving&hellip; 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