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how-to.html
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---
layout: default
title: "How-to"
permalink: how-to.html
group: "navigation"
order: 3
---
<script>
$(document).ready(function(){
function scrollToAnchor(aid){
var aTag = $("#"+ aid);
$('html, body').animate({
scrollTop: aTag.offset().top -90
}, 1000);
}
$("#scGeneral").click(function() {scrollToAnchor('general');});
$("#scParam").click(function() {scrollToAnchor('param');});
$("#scBest").click(function() {scrollToAnchor('bestPractice');});
$("#scToolConf").click(function() {scrollToAnchor('toolConf');});
$("#scPipeConf").click(function() {scrollToAnchor('pipelineConf');});
$("#scExamples").click(function() {scrollToAnchor('examples');});
$("#scOtherHelp").click(function() {scrollToAnchor('otherHelp');});
});
</script>
<div class="row">
<div class="col-md-3" style="padding-left: 0px; padding-top: 25px;" role="complementary">
<nav class=bs-docs-sidebar affix>
<ul class="nav bs-docs-sidenav affix">
<li><a id="scGeneral" class="description" style="text-decoration: none;" href="#">General gkno usage</a></li>
<li><a id="scParam" class="description" style="text-decoration: none;" href="#">Parameter sets</a></li>
<li><a id="scBest" class="description" style="text-decoration: none;" href="#">Best practice</a></li>
<li><a id="scToolConf" class="description" style="text-decoration: none;" href="#">Tool configuration files</a></li>
<li><a id="scPipeConf" class="description" style="text-decoration: none;" href="#">Pipeline configuration files</a></li>
<li><a id="scExamples" class="description" style="text-decoration: none;" href="#">Execution examples</a></li>
<li><a id="scOtherHelp" class="description" style="text-decoration: none;" href="#">Other help</a></li>
<ul>
</nav>
</div>
<div class="col-md-9" role="main">
<div class="section">
<h1 class="section-title">How to use gkno</h1>
<!-- General gkno usage -->
<div id="general" class="section-subtitle">General gkno usage</div>
<p class="description" id="indent"><a href="install.html">Installation:</a>
How to install gkno
</p>
<p class="description" id="indent"><a href="overview.html">Overview:</a>
How does <i>gkno</i> work?
</p>
<p class="description" id="indent"><a href="help.html">Pipeline help:</a>
How to find and use available gkno pipelines
</p>
<p class="description" id="indent"><a href="gkno-arguments.html">gkno arguments:</a>
Arguments applicable to all <i>gkno</i> pipelines
</p>
<p class="description" id="indent"><a href="parallel.html">Parallel execution:</a>
How to run <i>gkno</i> in parallel or on a cluster
</p>
<!-- Parameter sets -->
<div id="param" class="section-subtitle">Parameter sets</div>
<p class="description" id="indent"><a href="parameter-sets.html">What are they?</a>
What are parameter sets and how are they used?
</p>
<p class="description" id="indent"><a href="parameter-sets-config.html">In tool configuration files:</a>
How to define parameter sets in tool configuration files?
</p>
<p class="description" id="indent"><a href="coming-soon.html">In pipeline configuration files:</a>
How to define parameter sets in pipeline configuration files?
</p>
<p class="description" id="indent"><a href="test-parameter-sets.html">Test parameter sets:</a>
Check that gkno pipelines are functioning correctly
</p>
<p class="description" id="indent"><a href="create-parameter-sets.html">Create your own parameter sets:</a>
Generate your own parameter sets
</p>
<!-- Parameter sets -->
<div id="bestPractice" class="section-subtitle">Best practice guidelines</div>
<p class="description" id="indent"><a href="getting-started.html">Getting started:</a>
Find a pipeline starting a run
</p>
<!-- Tool configuration files -->
<div id="toolConf" class="section-subtitle">Tool configuration files</div>
<p class="description" id="indent"><a href="tool-required.html">Required attributes:</a>
Attributes required in a tool configuration file
</p>
<p class="description" id="indent"><a href="tool-arguments.html">Argument attributes:</a>
Attributes used to describe tool arguments
</p>
<p class="description" id="indent"><a href="parameter-sets-config.html">Parameter sets:</a>
How to define parameter sets in tool configuration files
</p>
<p class="description" id="indent"><a href="coming-soon.html">Create your own:</a>
A tutorial on creating a tool configuration file for your own tool
</p>
<!-- Pipeline configuration files -->
<div id="pipelineConf" class="section-subtitle">Pipeline configuration files</div>
<p class="description" id="indent"><a href="pipeline-config.html">Describe a pipeline:</a>
How to describe a gkno pipeline
</p>
<p class="description" id="indent"><a href="build-bwa-multi.html">Build a pipeline:</a>
Step-by-step guide to build the bwa-multi pipeline
</p>
<p class="description" id="indent"><a href="build-bwa-multi2.html">Build a pipeline:</a>
Guide to including pipelines in your new pipeline
</p>
<!-- Examples -->
<div id="examples" class="section-subtitle">Execution examples</div>
<p class="description" id="indent"><a href="examples.html">Examples:</a>
How to manipulate BAM files
</p>
<!-- Other useful links -->
<div id="otherHelp" class="section-subtitle">Other help</div>
<p class="description" id="indent"><a href="cshl.html">CSHL BAM tutorial:</a>
How to manipulate BAM files
</p>
<p class="description" id="indent"><a href="cshl_practical.html">CSHL Practical:</a>
Using gkno and iobio to generate and interrogate variant calls
</p>
<p class="description" id="indent"><a href="cshl_iobio.html">CSHL iobio practical:</a>
How to use the iobio tools for data QC and interrogation
</p>
</div>
</div>
</div>