{"id":968,"date":"2020-11-09T15:28:08","date_gmt":"2020-11-09T14:28:08","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=968"},"modified":"2022-04-06T14:50:08","modified_gmt":"2022-04-06T12:50:08","slug":"trainings-2019-toogle-practice","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-toogle\/trainings-2019-toogle-practice\/","title":{"rendered":"Trainings 2019 &#8211; TOOGLE &#8211; Practice"},"content":{"rendered":"<h2>TOGGLe Practice<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Hands On Lab Exercises for TOGGLe<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Related-course materials<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-toogle\/\">TOGGLe introduction<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">S\u00e9bastien RAVEL (sebastien.ravel@cirad.fr)<br \/>Christine TRANCHANT (christine.tranchant@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">15\/03\/2018<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">16\/04\/2019<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Summary<\/h3>\n<ul>\n<li><a href=\"#practice-1\">Creating your own workflow<\/a><\/li>\n<li><a href=\"#TPcluster\">TP on IRD cluster<\/a><\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-1\"><\/a><\/p>\n<h3>Creating your own workflow :<\/h3>\n<p>Practice 1 consists of using  base one pre-defined configuration file to build own workflow to use with TOGGLe.<\/p>\n<p><a target=\"_blank\" href=\"http:\/\/toggle.southgreen.fr\/manual\/completeManual\/\" rel=\"noopener noreferrer\">TOGGLe Manual Page<\/a><\/p>\n<p>The <a target=\"_blank\" href=\"https:\/\/raw.githubusercontent.com\/SouthGreenPlatform\/TOGGLE\/master\/exampleConfigs\/SNPdiscoveryPaired.config.txt\" rel=\"noopener noreferrer\">SNPdiscoveryPaired.config.txt<\/a> file is an example of how to customize your pipeline.<\/p>\n<h4><a name=\"order\"><\/a>Providing an order<\/h4>\n<p>The order of a pipeline is provided with key <b>$order<\/b>, base on the file, build new config file to run only from mapping to SNP calling.<\/p>\n<h4><a name=\"TPcluster\"><\/a>TP on IRD cluster<\/h4>\n<p>All input data:<\/p>\n<ul>\n<li>Input data : \/data2\/formation\/TPsnpSV\/fastqDir\/<\/li>\n<li>Reference : \/data2\/formation\/TPsnpSV\/reference.fasta<\/li>\n<li>Config file: \/data2\/formation\/TPsnpSV\/configFiles\/SNPdiscoveryPaired.config.txt<\/li>\n<\/ul>\n<p>To do:<\/p>\n<ul>\n<li>Create a &quot;formationX&quot; directory in your account<\/li>\n<li>Make \u00e0 copy for reference and input data into &quot;formationX&quot; directory (scp).<\/li>\n<li>Add the configuration file used by TOGGLe and change SGE key as below<\/li>\n<\/ul>\n<pre><code>$sge\n-q formation.q\n-b Y\n-cwd<\/code><\/pre>\n<h5>Connect to account and prepare datas:<\/h5>\n<ul>\n<li>Connect to the cluster:<\/li>\n<\/ul>\n<pre><code>    ssh -Y formationX@bioinfo-master.ird.fr<\/code><\/pre>\n<ul>\n<li>Launch a QRSH command:<\/li>\n<\/ul>\n<pre><code>    qrsh -q formation.q<\/code><\/pre>\n<ul>\n<li>Transfer the data from nas using SCP:<\/li>\n<\/ul>\n<pre><code>    scp -r nas:\/data2\/formation\/TPsnpSV .<\/code><\/pre>\n<ul>\n<li>Load TOGGLe tools:<\/li>\n<\/ul>\n<pre><code>    module load bioinfo\/TOGGLE\/0.3.6<\/code><\/pre>\n<hr \/>\n<h4>Launching an analysis<\/h4>\n<p>Use only one script to run all pipeline: <b>toggleGenerator.pl<\/b> script usage<\/p>\n<pre><code>  toggleGenerator.pl -d|--directory DIR -c|--config FILE -o|--outputdir DIR [-r|--reference FILE] [-k|--keyfile FILE] [-g|--gff FILE] [-nocheck|--nocheckFastq] [--help|-h]<\/code><\/pre>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Required named arguments:<\/th>\n<th style=\"text-align: left;\">description<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">-d \/ --directory DIR:<\/td>\n<td style=\"text-align: left;\">a folder with raw data to be treated (FASTQ, FASTQ.GZ, SAM, BAM, VCF)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-c \/ --config FILE:<\/td>\n<td style=\"text-align: left;\">generally it is the <em>software.config.txt<\/em> file but it can be any text file structured as shown below.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-o \/ --outputdir DIR:<\/td>\n<td style=\"text-align: left;\">the current version of TOGGLE will not modify the initial data folder but will create an output directory with all analyses in.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Optional named arguments:<\/th>\n<th style=\"text-align: left;\"><\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">-r \/ --reference FILE:<\/td>\n<td style=\"text-align: left;\">the reference FASTA file to be used. (1)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-g \/ -gff FILE:<\/td>\n<td style=\"text-align: left;\">the GFF file to be used for some tools.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-k \/ --keyfile FILE:<\/td>\n<td style=\"text-align: left;\">the keyfile use for demultiplexing step.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-nocheck \/ --nocheckFastq:<\/td>\n<td style=\"text-align: left;\">by default toggle checks if fastq format is correct in every file. This option allows to skip this step.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-report \/ --report:<\/td>\n<td style=\"text-align: left;\">generate pdf report <a href=\"{{ site.url }}\/manual\/completeManual\/#report\">(more info)<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">-h \/ --help:<\/td>\n<td style=\"text-align: left;\">show help message and exit<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>(1): If no database index exists, it will be automatically created if it is necessary. If the index already exists, they will not be re-created UNLESS the pipeline order (see below) expressively requests it (updating the index e.g.)<\/p>\n<p>All the the paths (files and folders) can be provided as absolute (\/home\/mylogin\/data\/myRef.fasta) or relative (..\/data\/myRef.fasta).<\/p>\n<p>Example of a command to run TOGGLe :<\/p>\n<pre><code>toggleGenerator.pl -d ~\/toggle\/fastq -c ~\/toggle\/SNPdiscoveryPaired.config.txt -o ~\/toggle\/outputRES -r ~\/toggle\/reference.fasta -nocheck -report<\/code><\/pre>\n<hr \/>\n<p>SOLUTIONS:<\/p>\n<pre><code>vim SNPdiscoveryPaired.config.txt\n qsub -q formation.q -b Y -N TOGGLE &quot;module load bioinfo\/TOGGLE\/0.3.6; toggleGenerator.pl -c \/home\/formationX\/TPsnpSV\/configFiles\/SNPdiscoveryPaired.config.txt -d \/home\/formationX\/TPsnpSV\/fastqDir\/ -r \/home\/formationX\/TPsnpSV\/reference.fasta -o \/home\/formationX\/outputTOGGLe -nocheck -report&quot;<\/code><\/pre>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Related courses : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-toogle\">TOGGLe<\/a><\/li>\n<\/ul>\n<hr \/>\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>TOGGLe Practice Description Hands On Lab Exercises for TOGGLe Related-course materials TOGGLe introduction Authors S\u00e9bastien RAVEL (sebastien.ravel@cirad.fr)Christine TRANCHANT (christine.tranchant@ird.fr) Creation&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-toogle\/trainings-2019-toogle-practice\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":966,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-968","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 - TOOGLE - Practice - 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-toogle\/trainings-2019-toogle-practice\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Trainings 2019 - TOOGLE - Practice - itrop\" \/>\n<meta property=\"og:description\" content=\"TOGGLe Practice Description Hands On Lab Exercises for TOGGLe Related-course materials TOGGLe introduction Authors S\u00e9bastien RAVEL (sebastien.ravel@cirad.fr)Christine TRANCHANT (christine.tranchant@ird.fr) Creation&hellip; 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