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docs/no_toc/02-why-containers.html

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-<p>Not only are our computers very unique at any one point in time, but as time moves forward computers and the software environments change very rapidly. Some of this happens through intentional installations of programs by computer users and some are automatic software updates that they may not be aware of that are instigated by the developers of the hardware and software that make up the computer.</p>
+<p>Not only are our computers very unique at any one point in time, but as time moves forward computers and the software environments change very rapidly. These changes might happen through intentional installations of programs by computer users. Some are changes users may not be aware of, which took place through automatic software updates that are instigated by the developers of the hardware and software that make up the computer.</p>
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-<p>If we control the computing environments, that is one less variable we need to deal with in our science. <strong>Control the computing environment = That much more reproducible science.</strong></p>
+<p>If we control the computing environments, that is one less variable we need to deal with in our science. <strong>Control the computing environment = much more reproducible science.</strong></p>
 <p>We could think of impractical ways to control our computing environment: We could have one laptop that we ship back and forth between all our collaborators. Although this may make the computing environment slightly more controlled, clearly it is not a practical solution.</p>
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-<p>And containerization works for aiding in reproducibility as shown by <span class="citation" data-cites="BeaulieuJones2017">(<a href="#ref-BeaulieuJones2017" role="doc-biblioref">Beaulieu-Jones and Greene 2017</a>)</span></p>
+<p>And containerization aids in reproducibility as shown by <span class="citation" data-cites="BeaulieuJones2017">(<a href="#ref-BeaulieuJones2017" role="doc-biblioref">Beaulieu-Jones and Greene 2017</a>)</span></p>
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-<p>When a container is used, an aspect of variability in scientific analysis – the computing environment – is controlled for, the results are more reproducible!</p>
+<p>When a container is used, an aspect of variability in scientific analysis – the computing environment – is controlled for, and as a result, the results are more reproducible!</p>
 </section><section id="top-reasons-for-containers" class="level2" data-number="2.3"><h2 data-number="2.3" class="anchored" data-anchor-id="top-reasons-for-containers">
 <span class="header-section-number">2.3</span> Top reasons for containers!</h2>
-<p>But more than this, there are even more benefits to using containers:</p>
-<p>Installing software can be a huge headache. Bioinformatics involves using software that is often fringe and developed and maintained by small teams – or sometimes the software isn’t maintained at all. This means installation can take a lot of valuable time that scientists often don’t have.</p>
+<p>Beside reasons stated above, there are even more benefits to using containers:</p>
+<p>Installing software can be a huge headache. Bioinformatics involves using software that is often fringe – developed and maintained by small teams – or sometimes the software isn’t maintained at all. This means installation can take a lot of valuable time that scientists often don’t have.</p>
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docs/no_toc/04-using-volumes.html

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 </section><section id="step-2-retry-calling-the-script" class="level4" data-number="4.1.1.1"><h4 data-number="4.1.1.1" class="anchored" data-anchor-id="step-2-retry-calling-the-script">
 <span class="header-section-number">4.1.1.1</span> Step 2: Retry calling the script</h4>
-<p><input type="checkbox"> Now we can run the following command but we will have to run <code>docker ps</code> or <code>docker container ls</code> and get the container ID we need to put here.</p>
+<p><input type="checkbox"> Now we can run the following command but we will have to run <code>docker ps</code> and get the container ID we need to put here.</p>
 <pre><code>docker exec -it &lt;REPLACE_WITH_CONTAINER_ID&gt; bash /home/run_analysis.sh</code></pre>
+<p>or in the exec tab of the container in Docker desktop app, run</p>
+<pre><code>bash /home/run_analysis.sh</code></pre>
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docs/no_toc/07-sharing-images.html

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 </section><section id="container-registries" class="level2" data-number="7.7"><h2 data-number="7.7" class="anchored" data-anchor-id="container-registries">
 <span class="header-section-number">7.7</span> Container Registries</h2>
-<p>To share our image with others (or ourselves), we can push it to an online repository. There are a lot of options for container registries. Container registries generally cross-compatible meaning you can pull the image from just about anywhere if you have the right command and software. You can use different container registries for different purposes.</p>
+<p>To share our image with others (or ourselves), we can push it to an online repository. There are a lot of options for container registries. Container registries are generally cross-compatible, meaning you can pull the image from just about anywhere if you have the right command and software. You can use different container registries for different purposes.</p>
 <p><a href="https://octopus.com/blog/top-8-container-registries">This article has a nice summary of some of the most popular ones</a>.</p>
 <p>And here’s a TL;DR of the most common registries:</p>
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 <p>We encourage you to consider what container registries work best for you specific project and team. Here’s a starter list of considerations you may want to think of, roughly in the order of importance.</p>
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 <li>If you have protected data and security concerns (like we discussed earlier in this chapter) you may need to pick a container registry that allows privacy and strong security.</li>
-<li>Price – not all container registries are free, but many of them are what kind of budget do you have for this purpose? Paying is generally not a necessity so don’t pay for a container registry subscription unless you need to.</li>
+<li>Price – not all container registries are free, but many of them aren’t. Think about what kind of budget do you have for specific purpose. Paying is generally not a necessity, so don’t pay for a container registry subscription unless you need to.</li>
 <li>What tools are you already using? For example GitHub, Azure, and AWS have their own container registries, if you already are using these services you may consider using their associated registry. (Note GitHub actions works quite seamlessly with Dockerhub, so personally I haven’t had a reason to use GitHub Container Registry but it is an option.)</li>
 <li>Is there an industry standard? Where are your collaborators or those at your institution storing your images?</li>
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docs/no_toc/09-troubleshooting.html

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 <li>Is there a software package I’m assuming the image/container has that it does not?</li>
 <li>Is there a typo?</li>
 <li>Am I missing a dependency? Make sure the dependency’s RUN steps come before the software package that needs it.</li>
-<li>If my docker image isn’t building is it because</li>
 <li>Did the base image I’m pulling from change or a file I’m <code>COPY</code>ing change? Do I need to use –no-cache to force a rebuild of everything so the changes are seen?</li>
 </ul>
 <p>Now you have the basics of using containers but this is really just the beginning! As you continue to work with containers you will encounter errors and need to troubleshoot. This table has a quick rundown on some of the most common errors:</p>