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      <h1>Using Bioconductor with containerit</h1>
                        <h4 class="author">Daniel Nüst</h4>
            
            <h4 class="date">2019-08-20</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/o2r-project/containerit/blob/master/vignettes/bioconductor.Rmd"><code>vignettes/bioconductor.Rmd</code></a></small>
      <div class="hidden name"><code>bioconductor.Rmd</code></div>

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<!-- Copyright 2019 Opening Reproducible Research (https://o2r.info) -->
<p><code>containerit</code> can install <a href="https://bioconductor.org"><em>Bioconductor</em></a> packages.</p>
<p>First we need a <em>Bioconductor</em> package locally:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="op">!</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(<span class="st">"BiocGenerics"</span>, <span class="dt">character.only =</span> <span class="ot">TRUE</span>)) BiocManager<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/BiocManager/topics/install">install</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"BiocGenerics"</span>))</a></code></pre></div>
<p>Then we load the package in a clean session and save the session, and only then create a <code>Dockerfile</code> from the session to not have <code>containerit</code>-specific dependencies in the <code>Dockerfile</code>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">info &lt;-<span class="st"> </span>callr<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/callr/topics/r">r_safe</a></span>(<span class="cf">function</span>() {</a>
<a class="sourceLine" id="cb2-2" data-line-number="2">      <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/message">suppressPackageStartupMessages</a></span>({</a>
<a class="sourceLine" id="cb2-3" data-line-number="3">        <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"BiocGenerics"</span>)</a>
<a class="sourceLine" id="cb2-4" data-line-number="4">        <span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/sessionInfo">sessionInfo</a></span>()</a>
<a class="sourceLine" id="cb2-5" data-line-number="5">      })</a>
<a class="sourceLine" id="cb2-6" data-line-number="6">    })</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"></a>
<a class="sourceLine" id="cb2-8" data-line-number="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"containerit"</span>)</a>
<a class="sourceLine" id="cb2-9" data-line-number="9">df &lt;-<span class="st"> </span><span class="kw"><a href="../reference/dockerfile.html">dockerfile</a></span>(<span class="dt">from =</span> info)</a></code></pre></div>
<pre><code>## INFO [2019-08-20 16:44:54] Going online? TRUE  ... to retrieve system dependencies (sysreq-api)
## INFO [2019-08-20 16:44:54] Trying to determine system requirements for the package(s) 'BiocGenerics' from sysreqs online DB
## INFO [2019-08-20 16:44:55] Adding Bioconductor packages: BiocGenerics
## INFO [2019-08-20 16:44:55] Created Dockerfile-Object based on sessionInfo</code></pre>
<p>A shortcut to this is provided with the function <code><a href="../reference/clean_session.html">containerit::clean_session(..)</a></code>:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">containerit<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/containerit/topics/clean_session">clean_session</a></span>(<span class="dt">expr =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/substitute">quote</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"BiocGenerics"</span>)))</a></code></pre></div>
<p>The created <code>Dockerfile</code> is:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">containerit<span class="op">::</span><span class="kw">print</span>(df)</a></code></pre></div>
<pre><code>FROM rocker/r-ver:3.6.1
LABEL maintainer="daniel"
RUN ["install2.r", "-r https://bioconductor.org/packages/3.9/bioc -r https://bioconductor.org/packages/3.9/data/annotation -r https://bioconductor.org/packages/3.9/data/experiment -r https://bioconductor.org/packages/3.9/workflows", "BiocGenerics"]
WORKDIR /payload/
CMD ["R"]</code></pre>
<p>Using a specific <a href="https://bioconductor.org/about/release-announcements/"><em>Bioconductor</em> version</a> or installing versioned packages is <strong>not supported</strong>.</p>
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