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<meta name="description" content=" Getting Started with Singularity and Singularity Hub Jan 26, 2017 / So you want to put your scientific analysis in a nice package and run it on a cluster? You’ve probably heard of the container technology called Docker?…too bad you can’t use it on your research cluster, because it introduces huge security issues. You’ve probably also heard of virtual machines, but most clusters won’t let you run those either. What options does this leave us? Oh wait, duh, you are reading this website. You already know the answer to this question.Getting StartedInstall SingularityThe easiest thing to do is to install Singularity on your local workstation: sudo apt-get update sudo apt-get -y install build-essential curl git sudo man vim autoconf libtool git clone https://github.com/singularityware/singularity.git cd singularity ./autogen.sh ./configure --prefix=/usr/local make sudo make installIf you have the unfortunate situation of using a Mac, or just need a virtual machine, then you will want to follow the instructions here. Basically, you need to install vagrant, virtual box, and then do this:vagrant init ubuntu/trusty64vagrant upvagrant ssh -c /bin/sh <<EOF sudo apt-get update sudo apt-get -y install build-essential curl git sudo man vim autoconf libtool git clone https://github.com/singularityware/singularity.git cd singularity ./autogen.sh ./configure --prefix=/usr/local make sudo make installEOFvagrant sshOnce you are in your Virtual Machine, or have Singularity up and running? Well, it’s time to go NUTS of course!A little about Singularity HubSingularity Hub is an online registry for images. This means that you can connect a Github repo containing a build specification file to this website, and the image is going to build for you automatically, and be available programatically! We can talk more about how that happens later. If you want some quick details, you should check out the Usage Docs on Singularity Hub.Make and run containersRun an imageFor this little preview, we are going to be first running an image, directly from Singularity Hub. This image is called vsoch/singularity-images and it’s associated with the equivalent Github repository.singularity run shub://vsoch/singularity-imagesShow Video Tutorial In the above, we use the Singularity Hub “unique resource identifier,” or uri, shub:// which tells the software to run an image from Singularity Hub.Create an imageRunning is great, but what if we want to mess around on the command line, using an image we’ve created ourselves? We can do that by creating an image:sudo singularity create analysis.imgsudo singularity import analysis.img docker://ubuntu:latestsingularity shell analysis.imgShow Video Tutorial In the above, we use the docker “unique resource identifier,” or uri, docker:// which tells the software to import a docker image.If we wanted to shell into the image and make it writable, meaning that we can write files and save changes, we would do this:sudo singularity shell --writable analysis.imgNote that we need sudo, and also note that you wouldn’t be able to do this on a research cluster, because you don’t have sudo.Create a reproducible imageThe problem with create an image, and then maybe writing stuff to it with --writable is that your work isn’t properly saved anywhere. You COULD ship and share the entire image, but that still doesn’t help to say what was done to it, and this is problematic. To help with this, we encourage you to create a build specification file, a file called Singularity. There are a few important sections you should know about. First, let’s look at a very simple file:Bootstrap: dockerFrom: ubuntu:latest%runscript echo "I can put here whatever I want to happen when the user runs my container!" exec echo "Hello Monsoir Meatball" "$@"%post echo "Here we are installing software and other dependencies for the container!" apt-get update apt-get install -y git The important things to note. The header section says that we want to Bootstrap a docker image, specifically From ubuntu:latest. No, you don’t actually need Docker installed to run this, because the layers are pulled from their API endpoint.Show Video Tutorial Once you have your bootstrap file, and you know how to use Github, you are really good to go. You can add the file to repository, connect it to Singularity Hub, and it will build automatically and be available via the shub:// endpoint. That’s it! Please enable JavaScript to view the comments powered by Disqus. Site last generated: Jul 26, 2017 ">
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<h1 class="post-title" itemprop="name headline">Getting Started with Singularity and Singularity Hub</h1>
<p class="post-meta"><time datetime="2017-01-26T00:00:00-05:00" itemprop="datePublished">Jan 26, 2017</time> /
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<p>So you want to put your scientific analysis in a nice package and run it on a cluster? You’ve probably heard of the container technology called Docker?</p>
<p><img src="/assets/img/tutorial/horsecarrot.png" /><br /></p>
<p>…too bad you can’t use it on your research cluster, because it introduces huge security issues. You’ve probably also heard of <a href="https://www.vagrantup.com/docs/virtualbox/" target="_blank">virtual machines</a>, but most clusters won’t let you run those either. What options does this leave us? Oh wait, duh, you are reading this website. You already know the answer to this question.</p>
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<div id="toc"></div>
<h2 id="getting-started">Getting Started</h2>
<h3 id="install-singularity">Install Singularity</h3>
<p>The easiest thing to do is to install Singularity on your local workstation:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code> sudo apt-get update
sudo apt-get -y install build-essential curl git sudo man vim autoconf libtool
git clone https://github.com/singularityware/singularity.git
<span class="nb">cd </span>singularity
./autogen.sh
./configure --prefix<span class="o">=</span>/usr/local
make
sudo make install
</code></pre>
</div>
<p>If you have the unfortunate situation of using a Mac, or just need a virtual machine, then you will want to follow the instructions <a href="http://singularity.lbl.gov/install-mac" target="_blank">here</a>. Basically, you need to install vagrant, virtual box, and then do this:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>vagrant init ubuntu/trusty64
vagrant up
vagrant ssh -c /bin/sh <span class="sh"><<EOF
sudo apt-get update
sudo apt-get -y install build-essential curl git sudo man vim autoconf libtool
git clone https://github.com/singularityware/singularity.git
cd singularity
./autogen.sh
./configure --prefix=/usr/local
make
sudo make install
EOF
</span>vagrant ssh
</code></pre>
</div>
<p>Once you are in your Virtual Machine, or have Singularity up and running? Well, it’s time to go NUTS of course!</p>
<h3 id="a-little-about-singularity-hub">A little about Singularity Hub</h3>
<p><a href="https://singularity-hub.org" target="_blank">Singularity Hub</a> is an online registry for images. This means that you can connect a Github repo containing a build specification file to this website, and the image is going to build for you automatically, and be available programatically! We can talk more about how that happens later. If you want some quick details, you should check out the <a href="https://www.singularity-hub.org/faq" target="_blank">Usage Docs</a> on Singularity Hub.</p>
<h2 id="make-and-run-containers">Make and run containers</h2>
<h3 id="run-an-image">Run an image</h3>
<p>For this little preview, we are going to be first running an image, directly from Singularity Hub. This image is called <a href="https://singularity-hub.org/collections/24/" target="_blank">vsoch/singularity-images</a> and it’s associated with <a href="https://www.github.com/vsoch/singularity-images" target="_blank">the equivalent Github repository.</a></p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>singularity run shub://vsoch/singularity-images
</code></pre>
</div>
<p><button style="color:white;margin-top:5px" class="btn btn-primary btn-lg asciinema-button" id="Pulling-and-running-a-Singularity-Hub-image">Show Video Tutorial</button></p>
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<asciinema-player src="assets/asciicast/shub-pull.json" poster="data:text/plain,Pulling and running a Singularity Hub image" title="Pulling and running a Singularity Hub image" author="[email protected]" cols="100" rows="41" speed="2.0" theme="asciinema">
</asciinema-player>
</div>
<p>In the above, we use the Singularity Hub “unique resource identifier,” or <code class="highlighter-rouge">uri</code>, <code class="highlighter-rouge">shub://</code> which tells the software to run an image from Singularity Hub.</p>
<h3 id="create-an-image">Create an image</h3>
<p>Running is great, but what if we want to mess around on the command line, using an image we’ve created ourselves? We can do that by creating an image:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>sudo singularity create analysis.img
sudo singularity import analysis.img docker://ubuntu:latest
singularity shell analysis.img
</code></pre>
</div>
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<p>In the above, we use the docker “unique resource identifier,” or <code class="highlighter-rouge">uri</code>, <code class="highlighter-rouge">docker://</code> which tells the software to import a docker image.</p>
<p>If we wanted to shell into the image and make it writable, meaning that we can write files and save changes, we would do this:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>sudo singularity shell --writable analysis.img
</code></pre>
</div>
<p>Note that we need sudo, and also note that you wouldn’t be able to do this on a research cluster, because you don’t have sudo.</p>
<h3 id="create-a-reproducible-image">Create a reproducible image</h3>
<p>The problem with create an image, and then maybe writing stuff to it with <code class="highlighter-rouge">--writable</code> is that your work isn’t properly saved anywhere. You COULD ship and share the entire image, but that still doesn’t help to say what was done to it, and this is problematic. To help with this, we encourage you to create a build specification file, a file called <code class="highlighter-rouge">Singularity</code>. There are a few important sections you should know about. First, let’s look at a very simple file:</p>
<div class="language-bash highlighter-rouge"><pre class="highlight"><code>Bootstrap: docker
From: ubuntu:latest
%runscript
<span class="nb">echo</span> <span class="s2">"I can put here whatever I want to happen when the user runs my container!"</span>
<span class="nb">exec echo</span> <span class="s2">"Hello Monsoir Meatball"</span> <span class="s2">"</span><span class="nv">$@</span><span class="s2">"</span>
%post
<span class="nb">echo</span> <span class="s2">"Here we are installing software and other dependencies for the container!"</span>
apt-get update
apt-get install -y git
</code></pre>
</div>
<p>The important things to note. The header section says that we want to <code class="highlighter-rouge">Bootstrap</code> a docker image, specifically <code class="highlighter-rouge">From</code> ubuntu:latest. No, you don’t actually need Docker installed to run this, because the layers are pulled from their API endpoint.</p>
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<p>Once you have your bootstrap file, and you know how to use Github, you are really good to go. You can add the file to repository, connect it to Singularity Hub, and it will build automatically and be available via the <code class="highlighter-rouge">shub://</code> endpoint. That’s it!</p>
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