{"id":993,"date":"2020-11-09T16:14:53","date_gmt":"2020-11-09T15:14:53","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=993"},"modified":"2022-04-06T14:50:08","modified_gmt":"2022-04-06T12:50:08","slug":"trainings-2019-workflows","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/","title":{"rendered":"Trainings 2019 &#8211; Workflows"},"content":{"rendered":"<h2>workflow manager<\/h2>\n<table class=\"table-contact\">\n<tr>\n<td><img decoding=\"async\" width=\"300%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png\" alt=\"\" \/>\n<\/td>\n<td>\nThis course introduces the 2 commonly used workflow managers in the South Green Bioformatics platform, both in a theoretical and practical way, with hands-on practice sessions. It will help you to quickly develop and run your own pipelines using these tools through an graphical user or command-line interface.\n<\/td>\n<\/tr>\n<\/table>\n<p><small>TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses<br \/>\nChristine Tranchant-Dubreuil, Sebastien Ravel, Cecile Monat, Gautier Sarah, Abdoulaye Di- allo, Laura Helou, Alexis Dereeper, Ndomassi Tando, Julie Orjuela-Bouniol, Francois Sabot. bioRxiv https: \/\/www.biorxiv.org\/content\/early\/2018\/01\/10\/245480.<\/p>\n<p><a href=\"http:\/\/toggle.southgreen.fr\">TOGGle website<\/a><\/p>\n<p><a href=\"http:\/\/galaxy.southgreen.fr\/galaxy\/\">Galaxy website<\/a><\/p>\n<h3>Prerequisites<\/h3>\n<p>Prior knowledge of workflow managers not necessary<br \/>\nBasic knowledge of Linux (Linux for dummies required) - TOGGLe practical<\/p>\n<div id=\"colonne1\">\n<h3>Program<\/h3>\n<ul>\n<li>Why using a workflow manager to analyse data ?<\/li>\n<li>How to perform an analysis ?<\/li>\n<li>How to create your own workflow ? <\/li>\n<li>How to execute it? <\/li>\n<li>Use case<\/li>\n<\/ul>\n<\/div>\n<div id=\"colonne2\">\n<h3>Learning objectives<\/h3>\n<ul>\n<li>Explaining what Workflow Managers are,<br \/>in which way they differ from each other.<\/li>\n<li>How you can use them in your research.<\/li>\n<li>Creating your own workflow<\/li>\n<li>Analysing your NGS data with Galaxy and TOGGLe<\/li>\n<\/ul>\n<\/div>\n<div id=\"colonne3\">\n<h3>Training material<\/h3>\n<ul>\n<li>Slides workflow managers : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/workflowManager-french.pdff\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>Slides galaxy : <a target=\"_blank\" href=\"http:\/\/galaxyproject.github.io\/training-material\/topics\/introduction\/slides\/introduction.html\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>Slides TOGGLe : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/\/Workflow2019-TOGGLe.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>Slides GIGWA : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/\/Gigwa_training.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>Practice Galaxy : <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/996-2\/\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>Practice TOGGLe : <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-toogle-practice\/\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<\/ul>\n<\/div>\n<div id=\"nextInline\" class=\"clearfix\">\n<h3>Instructors<\/h3>\n<ul>\n<li>Alexis Dereeper (AD) - alexis.dereeper@ird.fr<\/li>\n<li>Sebastien Ravel (SR) - sebastien.ravel@cirad.fr<\/li>\n<li>Julie Orjuela (JO) - julie.orjuela@ird.fr<\/li>\n<li>Christine Tranchant (CT) - christine.tranchant@ird.fr<\/li>\n<\/ul>\n<\/div>\n<h3>Trainings<\/h3>\n<table>\n<thead>\n<tr>\n<th><strong>Date<\/strong><\/th>\n<th><strong>Location<\/strong><\/th>\n<th><strong>Topics<\/strong><\/th>\n<th><strong>Participants<\/strong><\/th>\n<th><strong>Instructors<\/strong><\/th>\n<th><strong>Links<\/strong><\/th>\n<th><strong>Units<\/strong><\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>2019<\/td>\n<td>Montpellier, France<\/td>\n<td>TOGGLe<\/td>\n<td>15<\/td>\n<td>AD, SR, CT, JO<\/td>\n<td><\/td>\n<td>UMR DIADE, IPME, MIVEGEC, INTERTRYP, AGAP<\/td>\n<\/tr>\n<tr>\n<td>2018<\/td>\n<td>Montpellier, France<\/td>\n<td>TOGGLe<\/td>\n<td>20<\/td>\n<td>AD, SR, CT<\/td>\n<td><\/td>\n<td>UMR DIADE, IPME, MIVEGEC, INTERTRYP, AGAP<\/td>\n<\/tr>\n<tr>\n<td>2017<\/td>\n<td>Montpellier, France<\/td>\n<td>TOGGLe<\/td>\n<td>20<\/td>\n<td>CT, AD<\/td>\n<td><\/td>\n<td>UMR DIADE, IPME, MIVEGEC, INTERTRYP<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"<p>workflow manager This course introduces the 2 commonly used workflow managers in the South Green Bioformatics platform, both in a&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":1321,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-993","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>Trainings 2019 - Workflows - 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\/trainings-fr\/trainings-2019-workflows\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Trainings 2019 - Workflows - itrop\" \/>\n<meta property=\"og:description\" content=\"workflow manager This course introduces the 2 commonly used workflow managers in the South Green Bioformatics platform, both in a&hellip; Lire la suite\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/\" \/>\n<meta property=\"og:site_name\" content=\"itrop\" \/>\n<meta property=\"article:modified_time\" content=\"2022-04-06T12:50:08+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@ItropBioinfo\" \/>\n<meta name=\"twitter:label1\" content=\"Dur\u00e9e de lecture estim\u00e9e\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/\",\"url\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/\",\"name\":\"Trainings 2019 - Workflows - itrop\",\"isPartOf\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png\",\"datePublished\":\"2020-11-09T15:14:53+00:00\",\"dateModified\":\"2022-04-06T12:50:08+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#breadcrumb\"},\"inLanguage\":\"fr-FR\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"fr-FR\",\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#primaryimage\",\"url\":\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png\",\"contentUrl\":\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png\"},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Accueil\",\"item\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/front-page-2\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Trainings &#8211; FR\",\"item\":\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Trainings 2019 &#8211; Workflows\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/bioinfo.ird.fr\/#website\",\"url\":\"https:\/\/bioinfo.ird.fr\/\",\"name\":\"itrop\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/bioinfo.ird.fr\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"fr-FR\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/bioinfo.ird.fr\/#organization\",\"name\":\"i-Trop\",\"url\":\"https:\/\/bioinfo.ird.fr\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"fr-FR\",\"@id\":\"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png\",\"contentUrl\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png\",\"width\":1356,\"height\":1356,\"caption\":\"i-Trop\"},\"image\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/x.com\/ItropBioinfo\"]}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Trainings 2019 - Workflows - itrop","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/","og_locale":"fr_FR","og_type":"article","og_title":"Trainings 2019 - Workflows - itrop","og_description":"workflow manager This course introduces the 2 commonly used workflow managers in the South Green Bioformatics platform, both in a&hellip; Lire la suite","og_url":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/","og_site_name":"itrop","article_modified_time":"2022-04-06T12:50:08+00:00","og_image":[{"url":"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png","type":"","width":"","height":""}],"twitter_card":"summary_large_image","twitter_site":"@ItropBioinfo","twitter_misc":{"Dur\u00e9e de lecture estim\u00e9e":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/","url":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/","name":"Trainings 2019 - Workflows - itrop","isPartOf":{"@id":"https:\/\/bioinfo.ird.fr\/#website"},"primaryImageOfPage":{"@id":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#primaryimage"},"image":{"@id":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#primaryimage"},"thumbnailUrl":"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png","datePublished":"2020-11-09T15:14:53+00:00","dateModified":"2022-04-06T12:50:08+00:00","breadcrumb":{"@id":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#breadcrumb"},"inLanguage":"fr-FR","potentialAction":[{"@type":"ReadAction","target":["https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/"]}]},{"@type":"ImageObject","inLanguage":"fr-FR","@id":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#primaryimage","url":"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png","contentUrl":"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/trainings-workflowmanager.png"},{"@type":"BreadcrumbList","@id":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-workflows\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Accueil","item":"https:\/\/bioinfo.ird.fr\/index.php\/en\/front-page-2\/"},{"@type":"ListItem","position":2,"name":"Trainings &#8211; FR","item":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/"},{"@type":"ListItem","position":3,"name":"Trainings 2019 &#8211; Workflows"}]},{"@type":"WebSite","@id":"https:\/\/bioinfo.ird.fr\/#website","url":"https:\/\/bioinfo.ird.fr\/","name":"itrop","description":"","publisher":{"@id":"https:\/\/bioinfo.ird.fr\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/bioinfo.ird.fr\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"fr-FR"},{"@type":"Organization","@id":"https:\/\/bioinfo.ird.fr\/#organization","name":"i-Trop","url":"https:\/\/bioinfo.ird.fr\/","logo":{"@type":"ImageObject","inLanguage":"fr-FR","@id":"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/","url":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png","contentUrl":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png","width":1356,"height":1356,"caption":"i-Trop"},"image":{"@id":"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/"},"sameAs":["https:\/\/x.com\/ItropBioinfo"]}]}},"_links":{"self":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/993","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/comments?post=993"}],"version-history":[{"count":3,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/993\/revisions"}],"predecessor-version":[{"id":999,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/993\/revisions\/999"}],"up":[{"embeddable":true,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/1321"}],"wp:attachment":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/media?parent=993"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}