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<meta name="description" content=" Changing Existing Containers Container MetadataSingularity containers have two level of metadata - environment variables, and labels from the user and bootstrap process.EnvironmentIf you are importing a Docker container, the environment will be imported as well. If you want to define custom environment variables in your bootstrap recipe file Singularity you can do that like thisBootstrap:dockerFrom: ubuntu:latest%environmentVARIABLE_NAME=VARIABLE_VALUEForget something, or need a variable defined at runtime? You can set any variable you want inside the container by prefixing it with “SINGULARITYENV_”. It will be transposed automatically and the prefix will be stripped. For example, let’s say we want to set the variable HELLO to have value WORLD. We can do that as follows:$ SINGULARITYENV_HELLO=WORLD singularity exec -e centos7.img envHELLO=WORLDLD_LIBRARY_PATH=:/usr/local/lib:/usr/local/lib64SINGULARITY_NAME=test.imgPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/binPWD=/home/gmk/git/singularityLANG=en_US.UTF-8SHLVL=0SINGULARITY_INIT=1SINGULARITY_CONTAINER=test.imgNotice the -e? That is the argument (or --cleanenv) that specifies that we want to remove the host environment from the container. If we remove the -e, we will still pass forward HELLO=WORLD, and the list shown above, but we will also pass forward all the other environment variables from the host. Here is a command to directly echo the variable we define:$echo 'echo $HELLO' | SINGULARITYENV_HELLO=WORLD singularity exec centos7.img /bin/shWORLDIf you want to look at the environment inside a container, you can look inside the metadata env folder as follows:singularity exec centos7.img ls /.singularity.d/env01-base.sh 10-docker.sh 99-environment.shThe variables in 01-base.sh are a set of defaults set upon container creation, and the 10-docker.sh come from a Docker import.singularity exec centos7.img cat /.singularity.d/env/10-docker.shexport PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/binLabelsYour container stores metadata about it’s build, along with Docker labels. You can see the data as follows:singularity exec centos7.img cat /.singularity.d/labels.json{ "name": "CentOS Base Image", "build-date": "20170315", "vendor": "CentOS", "license": "GPLv2"}You can add custom labels to your container in a bootstrap file:Bootstrap: dockerFrom: ubuntu: latest%labelsAUTHOR Vanessasaur Previous Next Edit me Site last generated: Jul 26, 2017 ">
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<h2 id="container-metadata">Container Metadata</h2>
<p>Singularity containers have two level of metadata - environment variables, and labels from the user and bootstrap process.</p>
<h3 id="environment">Environment</h3>
<p>If you are importing a Docker container, the environment will be imported as well. If you want to define custom environment variables in your bootstrap recipe file <code class="highlighter-rouge">Singularity</code> you can do that like this</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>Bootstrap:docker
From: ubuntu:latest
%environment
<span class="nv">VARIABLE_NAME</span><span class="o">=</span>VARIABLE_VALUE
</code></pre>
</div>
<p>Forget something, or need a variable defined at runtime? You can set any variable you want inside the container by prefixing it with “SINGULARITYENV_”. It will be transposed automatically and the prefix will be stripped. For example, let’s say we want to set the variable <code class="highlighter-rouge">HELLO</code> to have value <code class="highlighter-rouge">WORLD</code>. We can do that as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="gp">$ </span><span class="nv">SINGULARITYENV_HELLO</span><span class="o">=</span>WORLD singularity <span class="nb">exec</span> -e centos7.img env
<span class="nv">HELLO</span><span class="o">=</span>WORLD
<span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span>:/usr/local/lib:/usr/local/lib64
<span class="nv">SINGULARITY_NAME</span><span class="o">=</span>test.img
<span class="nv">PATH</span><span class="o">=</span>/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
<span class="nv">PWD</span><span class="o">=</span>/home/gmk/git/singularity
<span class="nv">LANG</span><span class="o">=</span>en_US.UTF-8
<span class="nv">SHLVL</span><span class="o">=</span>0
<span class="nv">SINGULARITY_INIT</span><span class="o">=</span>1
<span class="nv">SINGULARITY_CONTAINER</span><span class="o">=</span>test.img
</code></pre>
</div>
<p>Notice the <code class="highlighter-rouge">-e</code>? That is the argument (or <code class="highlighter-rouge">--cleanenv</code>) that specifies that we want to remove the host environment from the container. If we remove the <code class="highlighter-rouge">-e</code>, we will still pass forward <code class="highlighter-rouge">HELLO=WORLD</code>, and the list shown above, but we will also pass forward all the other environment variables from the host. Here is a command to directly echo the variable we define:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code><span class="nv">$echo</span> <span class="s1">'echo $HELLO'</span> | <span class="nv">SINGULARITYENV_HELLO</span><span class="o">=</span>WORLD singularity <span class="nb">exec </span>centos7.img /bin/sh
WORLD
</code></pre>
</div>
<p>If you want to look at the environment inside a container, you can look inside the metadata env folder as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity <span class="nb">exec </span>centos7.img ls /.singularity.d/env
01-base.sh 10-docker.sh 99-environment.sh
</code></pre>
</div>
<p>The variables in <code class="highlighter-rouge">01-base.sh</code> are a set of defaults set upon container creation, and the <code class="highlighter-rouge">10-docker.sh</code> come from a Docker import.</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity <span class="nb">exec </span>centos7.img cat /.singularity.d/env/10-docker.sh
<span class="nb">export </span><span class="nv">PATH</span><span class="o">=</span>/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
</code></pre>
</div>
<h3 id="labels">Labels</h3>
<p>Your container stores metadata about it’s build, along with Docker labels. You can see the data as follows:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity <span class="nb">exec </span>centos7.img cat /.singularity.d/labels.json
<span class="o">{</span> <span class="s2">"name"</span>:
<span class="s2">"CentOS Base Image"</span>,
<span class="s2">"build-date"</span>: <span class="s2">"20170315"</span>,
<span class="s2">"vendor"</span>: <span class="s2">"CentOS"</span>,
<span class="s2">"license"</span>: <span class="s2">"GPLv2"</span>
<span class="o">}</span>
</code></pre>
</div>
<p>You can add custom labels to your container in a bootstrap file:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>Bootstrap: docker
From: ubuntu: latest
%labels
AUTHOR Vanessasaur
</code></pre>
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