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19 20 <link rel="index" title="Index" href="genindex.html" /> 21 <link rel="search" title="Search" href="search.html" /> 22 <link rel="next" title="Getting Started" href="getting_started.html" /> 23</head> 24 25<body class="wy-body-for-nav"> 26 <div class="wy-grid-for-nav"> 27 <nav data-toggle="wy-nav-shift" class="wy-nav-side"> 28 <div class="wy-side-scroll"> 29 <div class="wy-side-nav-search" > 30 31 32 33 <a href="#" class="icon icon-home"> 34 Batch 35 </a> 36<div role="search"> 37 <form id="rtd-search-form" class="wy-form" action="search.html" method="get"> 38 <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" /> 39 <input type="hidden" name="check_keywords" value="yes" /> 40 <input type="hidden" name="area" value="default" /> 41 </form> 42</div> 43 </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> 44 <ul> 45<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li> 46<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li> 47<li class="toctree-l1"><a class="reference internal" href="docker_resources.html">Docker Resources</a></li> 48<li class="toctree-l1"><a class="reference internal" href="service.html">Batch Service</a></li> 49<li class="toctree-l1"><a class="reference internal" href="cookbook.html">Cookbooks</a></li> 50<li class="toctree-l1"><a class="reference internal" href="api.html">Reference (Python API)</a></li> 51<li class="toctree-l1"><a class="reference internal" href="configuration_reference.html">Configuration Reference</a></li> 52<li class="toctree-l1"><a class="reference internal" href="advanced_search_help.html">Advanced UI Search Help</a></li> 53<li class="toctree-l1"><a class="reference internal" href="change_log.html">Python Version Compatibility Policy</a></li> 54<li class="toctree-l1"><a class="reference internal" href="change_log.html#change-log">Change Log</a></li> 55</ul> 56 57 </div> 58 </div> 59 </nav> 60 61 <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" > 62 <i data-toggle="wy-nav-top" class="fa fa-bars"></i> 63 <a href="#">Batch</a> 64 </nav> 65 66 <div class="wy-nav-content"> 67 <div class="rst-content"> 68 <div role="navigation" aria-label="Page navigation"> 69 <ul class="wy-breadcrumbs"> 70 <li><a href="#" class="icon icon-home" aria-label="Home"></a></li> 71 <li class="breadcrumb-item active">Batch</li> 72 <li class="wy-breadcrumbs-aside"> 73 <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a> 74 </li> 75 </ul> 76 <hr/> 77</div> 78 <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> 79 <div itemprop="articleBody"> 80 81 <section id="batch"> 82<h1>Batch<a class="headerlink" href="#batch" title="Permalink to this heading">ï</a></h1> 83<p>Batch is a Python module for creating and executing jobs. A job consists of a bash 84command to run as well as a specification of the resources required and some metadata. 85Batch allows you to easily build complicated computational pipelines with many jobs and numerous 86dependencies. Batches can either be executed locally or with the <a class="reference internal" href="service.html#sec-service"><span class="std std-ref">Batch Service</span></a>.</p> 87<img alt="_images/dags.008.png" src="_images/dags.008.png" /> 88</section> 89<section id="contents"> 90<h1>Contents<a class="headerlink" href="#contents" title="Permalink to this heading">ï</a></h1> 91<div class="toctree-wrapper compound"> 92<ul> 93<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a><ul> 94<li class="toctree-l2"><a class="reference internal" href="getting_started.html#installation">Installation</a></li> 95</ul> 96</li> 97<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a><ul> 98<li class="toctree-l2"><a class="reference internal" href="tutorial.html#import">Import</a></li> 99<li class="toctree-l2"><a class="reference internal" href="tutorial.html#f-strings">f-strings</a></li> 100<li class="toctree-l2"><a class="reference internal" href="tutorial.html#hello-world">Hello World</a></li> 101<li class="toctree-l2"><a class="reference internal" href="tutorial.html#file-dependencies">File Dependencies</a></li> 102<li class="toctree-l2"><a class="reference internal" href="tutorial.html#scatter-gather">Scatter / Gather</a></li> 103<li class="toctree-l2"><a class="reference internal" href="tutorial.html#nested-scatters">Nested Scatters</a></li> 104<li class="toctree-l2"><a class="reference internal" href="tutorial.html#input-files">Input Files</a></li> 105<li class="toctree-l2"><a class="reference internal" href="tutorial.html#output-files">Output Files</a></li> 106<li class="toctree-l2"><a class="reference internal" href="tutorial.html#resource-groups">Resource Groups</a></li> 107<li class="toctree-l2"><a class="reference internal" href="tutorial.html#resource-file-extensions">Resource File Extensions</a></li> 108<li class="toctree-l2"><a class="reference internal" href="tutorial.html#python-jobs">Python Jobs</a></li> 109<li class="toctree-l2"><a class="reference internal" href="tutorial.html#backends">
109Backends</a></li> 110</ul> 111</li> 112<li class="toctree-l1"><a class="reference internal" href="docker_resources.html">Docker Resources</a><ul> 113<li class="toctree-l2"><a class="reference internal" href="docker_resources.html#what-is-docker">What is Docker?</a></li> 114<li class="toctree-l2"><a class="reference internal" href="docker_resources.html#installation">Installation</a></li> 115<li class="toctree-l2"><a class="reference internal" href="docker_resources.html#creating-a-dockerfile">Creating a Dockerfile</a></li> 116<li class="toctree-l2"><a class="reference internal" href="docker_resources.html#building-images">Building Images</a></li> 117<li class="toctree-l2"><a class="reference internal" href="docker_resources.html#pushing-images">Pushing Images</a></li> 118</ul> 119</li> 120<li class="toctree-l1"><a class="reference internal" href="service.html">Batch Service</a><ul> 121<li class="toctree-l2"><a class="reference internal" href="service.html#what-is-the-batch-service">What is the Batch Service?</a></li> 122<li class="toctree-l2"><a class="reference internal" href="service.html#sign-up">Sign Up</a></li> 123<li class="toctree-l2"><a class="reference internal" href="service.html#file-localization">File Localization</a></li> 124<li class="toctree-l2"><a class="reference internal" href="service.html#service-accounts">Service Accounts</a></li> 125<li class="toctree-l2"><a class="reference internal" href="service.html#billing">Billing</a></li> 126<li class="toctree-l2"><a class="reference internal" href="service.html#setup">Setup</a></li> 127<li class="toctree-l2"><a class="reference internal" href="service.html#submitting-a-batch-to-the-service">Submitting a Batch to the Service</a></li> 128<li class="toctree-l2"><a class="reference internal" href="service.html#regions">Regions</a></li> 129<li class="toctree-l2"><a class="reference internal" href="service.html#using-the-ui">Using the UI</a></li> 130<li class="toctree-l2"><a class="reference internal" href="service.html#important-notes">Important Notes</a></li> 131</ul> 132</li> 133<li class="toctree-l1"><a class="reference internal" href="cookbook.html">Cookbooks</a><ul> 134<li class="toctree-l2"><a class="reference internal" href="cookbook/clumping.html">Clumping GWAS Results</a></li> 135<li class="toctree-l2"><a class="reference internal" href="cookbook/random_forest.html">Random Forest</a></li> 136</ul> 137</li> 138<li class="toctree-l1"><a class="reference internal" href="api.html">Reference (Python API)</a><ul> 139<li class="toctree-l2"><a class="reference internal" href="api.html#batches">Batches</a></li> 140<li class="toctree-l2"><a class="reference internal" href="api.html#resources">Resources</a></li> 141<li class="toctree-l2"><a class="reference internal" href="api.html#batch-pool-executor">Batch Pool Executor</a></li> 142<li class="toctree-l2"><a class="reference internal" href="api.html#backends">Backends</a></li> 143<li class="toctree-l2"><a class="reference internal" href="api.html#utilities">Utilities</a></li> 144</ul> 145</li> 146<li class="toctree-l1"><a class="reference internal" href="configuration_reference.html">Configuration Reference</a></li> 147<li class="toctree-l1"><a class="reference internal" href="advanced_search_help.html">Advanced UI Search Help</a><ul> 148<li class="toctree-l2"><a class="reference internal" href="advanced_search_help.html#exact-match-expression">Exact Match Expression</a></li> 149<li class="toctree-l2"><a class="reference internal" href="advanced_search_help.html#partial-match-expression">Partial Match Expression</a></li> 150<li class="toctree-l2"><a class="reference internal" href="advanced_search_help.html#keyword-expression">Keyword Expression</a></li> 151<li class="toctree-l2"><a class="reference internal" href="advanced_search_help.html#predefined-keyword-expression">Predefined Keyword Expression</a></li> 152<li class="toctree-l2"><a class="reference internal" href="advanced_search_help.html#combining-multiple-statements">Combining Multiple Statements</a></li> 153</ul> 154</li> 155<li class="toctree-l1"><a class="reference internal" href="change_log.html">Python Version Compatibility Policy</a></li> 156<li class="toctree-l1"><a class="reference internal" href="change_log.html#change-log">Change Log</a></li> 157</ul> 158</div> 159</section> 160<section id="indices-and-tables"> 161<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this heading">ï</a></h1> 162<ul class="simple"> 163<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li> 164<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li> 165</ul> 166</section> 167 168 169 </div> 170 </div> 171 <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer"> 172 <a href="getting_started.html" class="btn btn-neutral 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