<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Run in a Docker container • sen2r</title>
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/yeti/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><meta property="og:title" content="Run in a Docker container">
<meta property="og:description" content="sen2r">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
    

    <div class="container template-article">
      <header><div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">sen2r</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.6.0</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"></ul>
<ul class="nav navbar-nav navbar-right">
<li>
  <a href="../index.html">
    <span class="fa fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../reference/index.html">
    <span class="fa fa-file-code"></span>
     
     Reference
  </a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-book"></span>
     
     Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu">
<li>
      <a href="../articles/installation.html">Installation</a>
    </li>
    <li>
      <a href="../articles/docker.html">Run in a Docker container</a>
    </li>
    <li>
      <a href="../articles/sen2r_gui.html">Using sen2r() from the GUI</a>
    </li>
    <li>
      <a href="../articles/sen2r_cmd.html">Using sen2r() from the command line</a>
    </li>
    <li>
      <a href="../articles/outstructure.html">Output file structure</a>
    </li>
  </ul>
</li>
<li>
  <a href="../news/index.html">
    <span class="fa fa-newspaper"></span>
     
     Changelog
  </a>
</li>
<li>
  <a href="http://luigi.ranghetti.info" class="external-link">
    <span class="fa fa-user"></span>
     
  </a>
</li>
<li>
  <a href="https://github.com/ranghetti/sen2r/" class="external-link">
    <span class="fa fa-github fa-lg"></span>
     
  </a>
</li>
      </ul>
</div>
<!--/.nav-collapse -->
  </div>
<!--/.container -->
</div>
<!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Run in a Docker container</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/ranghetti/sen2r/blob/HEAD/vignettes/docker.Rmd" class="external-link"><code>vignettes/docker.Rmd</code></a></small>
      <div class="hidden name"><code>docker.Rmd</code></div>

    </div>

    
    
<p>A dockerised version of <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span>
is available <a href="https://hub.docker.com/r/ranghetti/sen2r" class="external-link">here</a>: it contains a
working RStudio environment with the package <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span>
and all its dependencies (both R packages and runtime dependencies). It
can be used in order to avoid troublings about compiling all the
required R packages, or in case of problems with runtime dependencies
(typically GDAL over Windows).</p>
<p>To use it:</p>
<ol style="list-style-type: decimal">
<li><p><a href="https://docs.docker.com/install" class="external-link">install Docker CE</a>
version 1.13 or higher;</p></li>
<li><p>read the docker documentation in <a href="https://docs.docker.com/get-started" class="external-link">Part 1</a>;</p></li>
<li>
<p>obtain the image of <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">docker</span> pull ranghetti/sen2r:latest</span></code></pre></div>
<p>where <code>latest</code> corresponds to the software version in
branch <a href="https://github.com/ranghetti/sen2r/tree/main" class="external-link">main</a>
(see <a href="https://hub.docker.com/repository/registry-1.docker.io/ranghetti/sen2r/tags" class="external-link">here</a>
all the available docker tags);</p>
</li>
<li>
<p>run the docker:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">docker</span> run <span class="at">--rm</span> <span class="at">-e</span> PASSWORD=sen2r <span class="at">-e</span> USERID=<span class="va">$(</span><span class="fu">id</span> <span class="at">-u</span><span class="va">)</span> <span class="at">-v</span> <span class="va">$(</span><span class="bu">pwd</span><span class="va">)</span>:/home/rstudio/host <span class="at">-p</span> 8777:8787 ranghetti/sen2r</span></code></pre></div>
<p>where:</p>
<ul>
<li>
<code>-e PASSWORD=sen2r</code> is the password to be used to
login;</li>
<li>
<code>-v $(pwd):/home/rstudio/host</code> means that the current
directory will be mounted in the docker, and its content will be
available in the subdirectory <code>host</code> of the docker folder
tree (to mount a different directory, replace <code>$(pwd)</code> with
the desired directory);</li>
<li>
<code>-p 8777:8787</code> means that the dockerised RStudio will be
accessible from port 8777 (change it to use a different port).</li>
</ul>
</li>
<li><p>access to the RStudio environment from
<code>http://localhost:8777</code>, logging in with user
<code>rstudio</code> and the password set as above;</p></li>
<li>
<p>for online use, add the user’s SciHub credentials using the GUI
or with the function:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://sen2r.ranghetti.info" class="external-link">sen2r</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/scihub_login.html">write_scihub_login</a></span><span class="op">(</span><span class="st">"&lt;scihub_username&gt;"</span>, <span class="st">"&lt;scihub_password&gt;"</span><span class="op">)</span></span></code></pre></div>
</li>
</ol>
</div>

  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

      </div>

</div>



      <footer><div class="copyright">
  <p></p>
<p>Developed by Luigi Ranghetti, Lorenzo Busetto.</p>
</div>

<div class="pkgdown">
  <p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer>
</div>

  


  

  </body>
</html>
