{"id":490,"date":"2020-11-03T12:26:57","date_gmt":"2020-11-03T11:26:57","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=490"},"modified":"2022-04-06T14:50:28","modified_gmt":"2022-04-06T12:50:28","slug":"git-for-dummies","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/git-for-dummies\/","title":{"rendered":"Tutorials &#8211; Git For Dummies"},"content":{"rendered":"<h2>Git for dummies<\/h2>\n<table class=\"table-contact\">\n<tr>\n<td><img decoding=\"async\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/trainings-linux.png\" alt=\"\" \/>\n<\/td>\n<td>\n<h1> Git For Dummies<\/h1>\n<p>\nThis page describes describes the main commands you need in order to use Git.\n<\/td>\n<\/tr>\n<\/table>\n<h3>Author(s)<\/h3>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Authors<\/th>\n<th style=\"text-align: left;\">Christine Tranchant-Dubreuil<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Research Unit<\/td>\n<td style=\"text-align: left;\">UMR DIADE<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Institut<\/td>\n<td style=\"text-align: left;\"><img decoding=\"async\" src=\"https:\/\/www.ird.fr\/extension\/ird\/design\/ird\/images\/picto\/logo_ird.png\" width=\"20%\"><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Keywords<\/h3>\n<p>git<\/p>\n<h3>Date<\/h3>\n<p>10\/03\/2017<\/p>\n<hr \/>\n<h2>Summary<\/h2>\n<ul>\n<li><a href=\"#clone\">Download the repository using the <code>git clone<\/code>command<\/a><\/li>\n<li><a href=\"#pull\">Update the downloaded repository using the <code>git pull<\/code> command<\/a><\/li>\n<li><a href=\"#file-add\">Add a file, commit and pull with <code>git add<\/code>, <code>git commit<\/code> and <code>git pull<\/code><\/a><\/li>\n<li><a href=\"#file-add\">Remove a file using <code>git rm<\/code><\/a><\/li>\n<li><a href=\"#branch\">Branching<\/a><\/li>\n<\/ul>\n<p><a name=\"clone\"><\/a><\/p>\n<h2>Download the repository using the <code>git clone<\/code>command<\/h2>\n<pre><code> git clone https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git &lt;directory name&gt;<\/code><\/pre>\n<pre><code>#Example\n[tranchant@master0 TOGGLE-ON-THE-FLY]$ git clone https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git .\nCloning into &#039;.&#039;...\nremote: Counting objects: 7945, done.\nremote: Compressing objects: 100% (124\/124), done.\nremote: Total 7945 (delta 78), reused 0 (delta 0), pack-reused 7820\nReceiving objects: 100% (7945\/7945), 170.06 MiB | 23.03 MiB\/s, done.\nResolving deltas: 100% (5503\/5503), done.\nChecking out files: 100% (364\/364), done.<\/code><\/pre>\n<p><a name=\"pull\"><\/a><\/p>\n<h2>Update the downloaded repository using the <code>git pull<\/code> command<\/h2>\n<p>update your copy of repository with the version on remote server<\/p>\n<pre><code> git pull https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git &lt;branch name&gt;<\/code><\/pre>\n<pre><code>#Example\n[tranchant@master0 TOGGLE-ON-THE-FLY]$ git pull https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git  master\nFrom https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV\n * branch            master     -&gt; FETCH_HEAD\nAlready up-to-date.<\/code><\/pre>\n<p><a name=\"file-add\"><\/a><\/p>\n<h2>Add a file, commit and pull with <code>git add<\/code>, <code>git commit<\/code> and <code>git pull<\/code><\/h2>\n<p>Don't forget to pull to download the latest changes before pushing<\/p>\n<h4>To add a file (a change) to your local index with <code>git add<\/code><\/h4>\n<pre><code>git add &lt;filename&gt;<\/code><\/pre>\n<h4>To actually commit these changes with <code>git commit<\/code><\/h4>\n<pre><code>git commit -m &quot;message&quot; &lt;file name&gt;<\/code><\/pre>\n<h4>To send those changes to your remote repository with <code>git pull<\/code><\/h4>\n<pre><code>git push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git &lt;branch_name&gt;<\/code><\/pre>\n<p>Example<\/p>\n<pre><code>[tranchant@master0 TOGGLE-ON-THE-FLY]$ git add update.txt\n\n[tranchant@master0 TOGGLE-ON-THE-FLY]$ git commit -m &quot;Adding update.txt file&quot; update.txt\n[master ebb0a1c] Adding update.txt file\n 1 file changed, 0 insertions(+), 0 deletions(-)\n create mode 100644 update.txt\n\n[tranchant@master0 TOGGLE-ON-THE-FLY]$ git push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git master\nCounting objects: 3, done.\nDelta compression using up to 16 threads.\nCompressing objects: 100% (2\/2), done.\nWriting objects: 100% (2\/2), 271 bytes | 0 bytes\/s, done.\nTotal 2 (delta 1), reused 0 (delta 0)\nremote: Resolving deltas: 100% (1\/1), completed with 1 local objects.\nTo https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git\n   fec3a1f..ebb0a1c  master -&gt; master<\/code><\/pre>\n<p><a name=\"file-rm\"><\/a><\/p>\n<h2>Remove a file using <code>git rm<\/code><\/h2>\n<pre><code>git rm &lt;file name&gt;<\/code><\/pre>\n<pre><code>[tranchant@master0 TOGGLE-ON-THE-FLY]$ git rm update.txt\nrm &#039;update.txt&#039;\n\n[tranchant@master0 TOGGLE-ON-THE-FLY]$ git commit -m &quot;Remove update.txt file&quot; update.txt\n[master 9fa50b4] Remove update.txt file\n 1 file changed, 0 insertions(+), 0 deletions(-)\n delete mode 100644 update.txt\n\n[tranchant@master0 TOGGLE-ON-THE-FLY]$ git push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git master\nCounting objects: 3, done.\nDelta compression using up to 16 threads.\nCompressing objects: 100% (2\/2), done.\nWriting objects: 100% (2\/2), 236 bytes | 0 bytes\/s, done.\nTotal 2 (delta 1), reused 0 (delta 0)\nremote: Resolving deltas: 100% (1\/1), completed with 1 local objects.\nTo https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git\n   ebb0a1c..9fa50b4  master -&gt; master<\/code><\/pre>\n<p><a name=\"branch\"><\/a><\/p>\n<h2>Branching<\/h2>\n<p>Branches are used to develop new features or modify codes isolated from each other. The <em>master<\/em> branch is the &quot;default&quot; branch when a repository is created. Use other branches for development and merge them back to the master branch.<\/p>\n<h4>View all branches that were ever checked out on your local copy using <code> git branch <\/code><\/h4>\n<pre><code>git branch<\/code><\/pre>\n<pre><code>[tranchant@master0 TOGGLE-ON-THE-FLY]$ git branch\n* master<\/code><\/pre>\n<ul>\n<li>indicates the branch used actually<\/li>\n<\/ul>\n<h4>View all distant branches using <code> git branch <\/code><\/h4>\n<pre><code>git branch -r<\/code><\/pre>\n<pre><code>[tranchant@master0 TOGGLE-ON-THE-FLY]$ git branch -r\n  origin\/HEAD -&gt; origin\/master\n  origin\/master\n  origin\/picardtools-samtofastq\n  origin\/samtoolsBlocks\n  origin\/structuralVariant\n  origin\/tgicl\n  origin\/transabyss\n  origin\/trinity<\/code><\/pre>\n<h3>Create your own branch on your local copy then transfer it on remote server<\/h3>\n<p>Create the branch<\/p>\n<pre><code>git branch &lt;branch name&gt;<\/code><\/pre>\n<p>Move into this branch<\/p>\n<pre><code>git checkout &lt;branch name&gt;<\/code><\/pre>\n<p>Commit the changes<\/p>\n<pre><code>git commit -m &quot;mon commentaire&quot;<\/code><\/pre>\n<p>Push this local branch on the remote server<\/p>\n<pre><code> git push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git nom_branche<\/code><\/pre>\n<h3>Get a distant branch on the local repository if the branch don't exist locally<\/h3>\n<h4>Method 1<\/h4>\n<pre><code>git checkout &lt;remote branch name&gt;\ngit pull https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git nom_branche_distante `<\/code><\/pre>\n<h4>Method 2<\/h4>\n<pre><code>git branch &lt;remote branch name&gt;\ngit pull https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git &lt;remote branch name&gt;\ngit checkout &lt;remote branch name&gt;<\/code><\/pre>\n<h3>To merge another branch  (ex: samtoolsBlock)  into your active branch (e.g. master)<\/h3>\n<h4>Move into the &quot;active&quot; branch (e.g. master)<\/h4>\n<pre><code>git checkout master<\/code><\/pre>\n<h4>Update your local repository to the newest commit,<\/h4>\n<pre><code>git pull https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git master<\/code><\/pre>\n<h4>Merging<\/h4>\n<pre><code>git merge samtoolsBlock<\/code><\/pre>\n<h4>Check and resolve the conflicts generated<\/h4>\n<p>You are responsible to merge those conflicts manually by editing the files shown by <code>git status<\/code>.<\/p>\n<pre><code> git status<\/code><\/pre>\n<h4>Commit and push the changes and the merge on the distant server<\/h4>\n<pre><code> git commit -m &quot;Branch merging samtoolsBlock-master&quot; -a\n git push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git master `<\/code><\/pre>\n<h3>Remove a branche<\/h3>\n<h4>on the remote server<\/h4>\n<pre><code> git push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git :nom_branche_a_suppr `<\/code><\/pre>\n<h4>on our local copy<\/h4>\n<pre><code>git branch nom-branche_a_suppr -d<\/code><\/pre>\n<h2>Back to the change just before the last commit without losing the work done<\/h2>\n<pre><code># create one branch\ngit branch readDir\n\n# move on this branch\ngit checkout readDir\n\n# push\ngit push https:\/\/github.com\/SouthGreenPlatform\/TOGGLE-DEV.git readDir `\n\n# back to the former branch\ngit checkout dev\n\n# Revert the commit (number given on the terminal)\ngit revert d10a97d\n\n# Push\ngit push\n\n# Back to the branch\ngit checkout readDir<\/code><\/pre>\n<h2>+DIVERSES COMMANDES+<\/h2>\n<p>To get status<\/p>\n<pre><code>git status<\/code><\/pre>\n<p>To get log<\/p>\n<pre><code>git log\ngit log --graph --pretty=format:&#039;%C(red)%h%Creset -%C(yellow)%d%Creset %s %C(green)(%cr) %C(bold blue)&lt;%an&gt;%Creset&#039; --abbrev-commit<\/code><\/pre>\n<p>Pour mettre la commande du dessus en alias dans git (exemple avec git lg)<br \/>\n<code> git config --global alias.lg &quot;log --color --graph --pretty=format:&#039;%C(red)%h%Creset -%C(yellow)%d%Creset %s %C(green)(%cr) %C(bold blue)&lt;%an&gt;%Creset&#039; --abbrev-commit&quot; <\/code><\/p>\n<ul>\n<li>pour virer un fichier du git quand il est trop gros (et qu'on ne peut plus pusher)<\/li>\n<\/ul>\n<p><code> git filter-branch --index-filter &#039;git rm --cached --ignore-unmatch DATA\/expectedData\/snpEffdata\/MSU6.1\/sequences.fa&#039; --prune-empty --tag-name-filter cat -- --all <\/code><\/p>\n<h2>Docs:<\/h2>\n<blockquote>\n<p><a href=\"https:\/\/ccwiki.in2p3.fr\/developpements:formation:git\">https:\/\/ccwiki.in2p3.fr\/developpements:formation:git<\/a><br \/>\n<a href=\"http:\/\/www.moussu.fr\/git\/\">http:\/\/www.moussu.fr\/git\/<\/a><\/p>\n<\/blockquote>\n","protected":false},"excerpt":{"rendered":"<p>Git for dummies Git For Dummies This page describes describes the main commands you need in order to use Git.&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/git-for-dummies\/\">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-490","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 - Git For Dummies - 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\/git-for-dummies\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorials - Git For Dummies - itrop\" \/>\n<meta property=\"og:description\" content=\"Git for dummies Git For Dummies This page describes describes the main commands you need in order to use Git.&hellip; 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