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README.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta name="viewport" content="width=device-width, initial-scale=1">
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line-height: 1.1;
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margin-bottom: 16px;
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margin: 16px 0;
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padding-left: 2em;
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margin-bottom: 0;
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margin-bottom: 16px;
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padding: 0 15px;
color: #777;
border-left: 4px solid #ddd;
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blockquote>:last-child {
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width: 100%;
overflow: auto;
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word-break: keep-all;
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font-weight: bold;
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table td {
padding: 6px 13px;
border: 1px solid #ddd;
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background-color: #fff;
border-top: 1px solid #ccc;
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background-color: #f8f8f8;
}
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max-width: 100%;
box-sizing: content-box;
background-color: #fff;
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code {
padding: 0;
padding-top: 0.2em;
padding-bottom: 0.2em;
margin: 0;
font-size: 85%;
background-color: rgba(0,0,0,0.04);
border-radius: 3px;
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code:before,
code:after {
letter-spacing: -0.2em;
content: "\00a0";
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margin: 0;
font-size: 100%;
word-break: normal;
white-space: pre;
background: transparent;
border: 0;
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margin-bottom: 16px;
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padding: 16px;
overflow: auto;
font-size: 85%;
line-height: 1.45;
background-color: #f7f7f7;
border-radius: 3px;
}
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margin-bottom: 0;
word-break: normal;
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word-wrap: normal;
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display: inline;
max-width: initial;
padding: 0;
margin: 0;
overflow: initial;
line-height: inherit;
word-wrap: normal;
background-color: transparent;
border: 0;
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pre code:after {
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font-size: 11px;
line-height: 10px;
color: #555;
vertical-align: middle;
background-color: #fcfcfc;
border: solid 1px #ccc;
border-bottom-color: #bbb;
border-radius: 3px;
box-shadow: inset 0 -1px 0 #bbb;
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font-weight: bold;
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font-weight: bold;
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font-style: italic;
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line-height: 10px;
color: #555;
vertical-align: middle;
background-color: #fcfcfc;
border: solid 1px #ccc;
border-bottom-color: #bbb;
border-radius: 3px;
box-shadow: inset 0 -1px 0 #bbb;
}
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margin-top: 3px;
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<h1 id="welcome-to-datelifes-docker-github-repository">Welcome to DateLife’s Docker GitHub repository!</h1>
<p><img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Pulls" /></p>
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<p><code>datelife</code> is a software that gets all available information on time of divergence of a group of lineages, and uses this information to date a phylogenetic tree. Its functionalities can be accessed via the <a href="https://github.com/phylotastic/datelife"><code>datelife</code> R package</a>, or through <a href="http://datelife.opentreeoflife.org/query"><code>datelife</code>’s website</a>, which is <a href="https://github.com/phylotastic/datelifeweb">constructed as an R shiny application</a> and is containerized with <a href="https://www.docker.com/?utm_source=google&utm_medium=cpc&utm_campaign=dockerhomepage&utm_content=namer&utm_term=dockerhomepage&utm_budget=growth&gclid=CjwKCAjw7--KBhAMEiwAxfpkWMXM6XbTANoSspqojqsXX7dBeTm13Yc7lwzn8kz7iAWAT_m0fEo9MRoCq9MQAvD_BwE">Docker</a>, i.e. “dockerized”, as <a href="https://www.r-bloggers.com/2021/05/dockerizing-shiny-applications/">explained here</a>.</p>
<p>This repository hosts the instructions for “dockerizing” <code>datelife</code>, which we whipped up by following diverse <a href="#resources">valuable resources</a>. The <code>datelife</code> Docker allows anyone to set up their own server for the <code>datelife</code> web app anywhere. There are a few alternative ways to do this. For all of them you require <a href="https://www.docker.com/products/docker-desktop">Docker Desktop installed</a>.</p>
<p>Table of Contents:</p>
<p><a href="#1-using-a-prebuilt-datelife-docker-image">1. Setting up a prebuilt <code>datelife</code> image</a></p>
<p><a href="#docker-image-datelife-v050-about"> • Docker image datelife v0.5.0 about</a></p>
<p><a href="#2-building-your-own-datelife-docker-image">2. Building a local <code>datelife</code> image</a></p>
<p><a href="#3-running-multiple-instances">3. Running multiple instances of the <code>datelife</code> shiny app</a></p>
<p><a href="#4-swarm">4. Using swarm</a></p>
<p><a href="#resources">Resources</a></p>
<p><br><br></p>
<h2 id="1-using-a-prebuilt-datelife-docker-image">1. Using a prebuilt DateLife Docker image</h2>
<p>Ideally, the latest <code>datelife</code> Docker image automatically builds and uploads to <a href="https://hub.docker.com/r/bomeara/datelife/dockerfile">bomeara/datelife’s Docker Hub (the Docker cloud)</a> with pushes to <a href="https://github.com/phylotastic/datelifedocker">this repository (the GitHub phylotastic/datelifedocker repo)</a>. However, due to changes on Docker’s product subscriptions, automatic builds are not available for the moment (last updated on Oct 22, 2021). <code>datelife v0.5.0</code> is the latest, locally built, manually uploaded Docker image, and is hosted at <a href="https://hub.docker.com/repository/docker/lunasare/datelife">lunasare/datelife’s Docker Hub</a>.</p>
<!-- Look at this for list styling: https://gist.github.com/bertobox/3503850#gistcomment-1213320 -->
<ul style="list-style-type:none;">
<li>
<p>1.1. To download the prebuilt <code>datelife</code> Docker image from Docker Hub you need <a href="https://www.docker.com/products/docker-desktop">Docker desktop installed</a>. Then, from terminal use the <code>docker pull</code> command:</p>
</li>
<br>
<pre class="shell"><code> # docker pull bomeara/datelife
docker pull lunasare/datelife:v0.5.0
</code></pre>
<li>
<p>1.2. Now, you can start the image using <code>docker run</code>. You can do this in “bash mode” so you can look around (i.e., in the /srv dir for the shiny app):</p>
</li>
<br>
<pre class="shell"><code> # docker run -t -i -p 80:3838 bomeara/datelife sh -c '/bin/bash'
docker run -t -i -p 80:3838 lunasare/datelife:v0.5.0 sh -c '/bin/bash'
</code></pre>
<p>Once you’ve finished looking around, just type <code>exit</code> and you will be logged out.</p>
<li>
<p>1.3. To start the image just in serve mode, do:</p>
</li>
<br>
<pre class="shell"><code> # docker run -t -i -d -p 80:3838 bomeara/datelife
docker run -t -i -d -p 80:3838 lunasare/datelife:v0.5.0
</code></pre>
<p>Go to <a href="http://localhost">http://localhost</a> on any browser to checkout your Datelife website and shiny app running.</p>
<p>Argument <code>-d</code> is optional, it stands for <code>--detach</code>, allowing you to keep on using your terminal while the DateLife website is being served.</p>
</ul>
<h3 id="docker-image-datelife-v050-about">Docker image datelife v0.5.0 about</h3>
<details>
<summary>Information on R packages used</summary>
<p>Obtained with R by running the following from the <a href="https://github.com/phylotastic/datelifeweb">datelifeweb</a> project in RStudio:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>renv<span class="op">::</span><span class="kw">init</span>()</span>
<span id="cb4-2"><a href="#cb4-2"></a>deps <-<span class="st"> </span><span class="kw">unique</span>(renv<span class="op">::</span><span class="kw">dependencies</span>()[,<span class="st">"Package"</span>])</span>
<span id="cb4-3"><a href="#cb4-3"></a>vers <-<span class="st"> </span><span class="kw">structure</span>(<span class="kw">lapply</span>(deps[<span class="kw">order</span>(deps)], packageVersion), <span class="dt">names =</span> deps[<span class="kw">order</span>(deps)])</span>
<span id="cb4-4"><a href="#cb4-4"></a>vers</span></code></pre></div>
<pre><code>$ape
[1] ‘5.5’
$datelife
[1] ‘0.5.0’
$datelifeplot
[1] ‘0.1.0’
$devtools
[1] ‘2.4.2’
$future
[1] ‘1.22.1’
$phangorn
[1] ‘2.7.1’
$phyloch
[1] ‘1.5.5’
$promises
[1] ‘1.2.0.1’
$renv
[1] ‘0.14.0’
$shiny
[1] ‘1.6.0’
$shinycssloaders
[1] ‘1.0.0’
$strap
[1] ‘1.4’
$stringr
[1] ‘1.4.0’
$utils
[1] ‘4.1.0’
</code></pre>
</details>
<details>
<summary>Information on Docker software</summary>
<p>Obtained with <code>docker version</code> command from the terminal:</p>
<pre class="shell"><code>Client: Docker Engine - Community
Cloud integration: 1.0.7
Version: 20.10.2
API version: 1.41
Go version: go1.13.15
Git commit: 2291f61
Built: Mon Dec 28 16:12:42 2020
OS/Arch: darwin/amd64
Context: default
Experimental: true
Server: Docker Engine - Community
Engine:
Version: 20.10.2
API version: 1.41 (minimum version 1.12)
Go version: go1.13.15
Git commit: 8891c58
Built: Mon Dec 28 16:15:28 2020
OS/Arch: linux/amd64
Experimental: true
containerd:
Version: 1.4.3
GitCommit: 269548fa27e0089a8b8278fc4fc781d7f65a939b
runc:
Version: 1.0.0-rc92
GitCommit: ff819c7e9184c13b7c2607fe6c30ae19403a7aff
docker-init:
Version: 0.19.0
GitCommit: de40ad0
</code></pre>
</details>
<p><br><br></p>
<h2 id="2-building-your-own-datelife-docker-image">2. Building your own DateLife Docker image</h2>
<p>This is the option for developers, and local debugging. If you tried setting up a prebuilt Docker image and it fails, you should try this.</p>
<ul style="list-style-type:none;">
<li>
<p>2.1. Make sure you have <a href="https://www.docker.com/products/docker-desktop">Docker desktop installed</a>. Then, download the <a href="https://github.com/phylotastic/datelifedocker">datelifedocker repository</a> to your computer. One way is to type from the terminal:</p>
</li>
<br>
<pre class="shell"><code> git clone https://github.com/phylotastic/datelifedocker.git
</code></pre>
<li>
<p>2.2. Change directories to your newly created datelifedocker directory using <code>cd your_path/datelifedocker</code>, and build the DateLife Docker image with:</p>
</li>
<br>
<pre class="shell"><code> docker build -t datelife:[optional tag] .
</code></pre>
<p>To build with <em>no cache</em> (that is, rebuilding the image from scratch) type <code>docker build -t datelife --no-cache .</code></p>
<p>Note! Building with <em>no cache</em> will take about <strong>2hrs and 36 min</strong> to run.</p>
<li>
<p>2.3 Now you can start the DateLife server from your newly created Docker image with:</p>
</li>
<br>
<pre class="shell"><code> docker run -t -i -p 80:3838 datelife:[optional tag]
</code></pre>
<p>Go to <a href="http://localhost">http://localhost</a> on any browser to checkout your Datelife shiny app running.</p>
<p>To stop serving, type <code>Ctrl + c</code> or <code>exit</code></p>
<li>
<p>2.4. To explore the contents of the DateLife Docker image on terminal, you can do:</p>
</li>
<br>
<pre class="shell"><code>docker run -t -i datelife:[optional tag] sh -c '/bin/bash'
</code></pre>
<p>If you want to explore a particular container, first list them all with <code>docker container ls</code>, and identify the <code>container-name</code> of the one you are interested in.</p>
<p>Then restart your container and execute it with:</p>
<pre class="shell"><code>docker container restart <container-name>
docker exec -it <container-name> sh -c '/bin/bash'
</code></pre>
<p>For more tips see <a href="https://stackoverflow.com/questions/30172605/how-do-i-get-into-a-docker-containers-shell">how-do-i-get-into-a-docker-containers-shell</a> and <a href="https://towardsdatascience.com/15-docker-commands-you-should-know-970ea5203421">15-docker-commands-you-should-know</a>.</p>
<li>
<p>2.5. After building and making changes, you can push (if you have permissions) the new <code>datelife</code> Docker image to Docker hub with:</p>
</li>
<br>
<pre class="shell"><code> docker tag datelife:[version number] lunasare/datelife:[version number]
docker login
docker push lunasare/datelife:[version number]
</code></pre>
<p>Note! If you make any important changes to the <code>dockerfile</code>, please bump its version and document the changes on the section <a href="#docker-image-datelife-v050-about">Docker image DateLife</a> of this README.</p>
</ul>
<p><br><br></p>
<h2 id="3-running-multiple-instances">3. Running multiple instances</h2>
<p>You can run multiple shiny app instances with:</p>
<pre class="shell"><code> docker-compose up -d --scale datelife=10 # for ten instances
</code></pre>
<p><br><br></p>
<h2 id="4-swarm">4. Swarm</h2>
<ul style="list-style-type:none;">
<li>
<p>4.1. Go to node where swarm is being managed. You can change the number of workers in replicas in the <code>docker-compose-swarm.yml</code> file.</p>
</li>
<br>
<pre class="shell"><code> sudo docker stack deploy --compose-file docker-compose-swarm.yml datelife
</code></pre>
<li>
<p>4.2. See how it’s doing with</p>
</li>
<br>
<pre class="shell"><code> sudo docker stack services datelife
</code></pre>
<li>
<p>4.3. And stop it with</p>
</li>
<br>
<pre class="shell"><code> sudo docker stack rm datelife
</code></pre>
<p>For domain, *, @, www all resolve to <code>datelife19.campus.utk.edu.</code> (yes, with a period after edu) using CNAME</p>
</ul>
<p><br><br></p>
<h2 id="resources">Resources</h2>
<ul>
<li><a href="https://www.r-bloggers.com/2021/05/dockerizing-shiny-applications/">https://www.r-bloggers.com/2021/05/dockerizing-shiny-applications/</a></li>
<li><a href="https://github.com/flaviobarros/shiny-wordcloud/blob/master/Dockerfile">https://github.com/flaviobarros/shiny-wordcloud/blob/master/Dockerfile</a></li>
<li><a href="https://www.statworx.com/at/blog/how-to-dockerize-shinyapps/">https://www.statworx.com/at/blog/how-to-dockerize-shinyapps/</a></li>
<li><a href="https://www.youtube.com/watch?v=ARd5IldVFUs">https://www.youtube.com/watch?v=ARd5IldVFUs</a></li>
<li><a href="https://hub.docker.com/u/rocker">https://hub.docker.com/u/rocker</a></li>
<li><a href="https://www.dabbleofdevops.com/blog/deploy-rshiny-with-the-rocker-shiny-docker-image">https://www.dabbleofdevops.com/blog/deploy-rshiny-with-the-rocker-shiny-docker-image</a></li>
<li><a href="https://blog.sellorm.com/2021/04/25/shiny-app-in-docker/">https://blog.sellorm.com/2021/04/25/shiny-app-in-docker/</a></li>
<li><a href="https://juanitorduz.github.io/dockerize-a-shinyapp/">https://juanitorduz.github.io/dockerize-a-shinyapp/</a></li>
<li><a href="https://bhoom.wordpress.com/2020/06/18/using-multiple-r-versions-with-docker-rocker-rstudio-project/">https://bhoom.wordpress.com/2020/06/18/using-multiple-r-versions-with-docker-rocker-rstudio-project/</a></li>
<li><a href="https://githubmemory.com/repo/rocker-org/shiny/issues/92">https://githubmemory.com/repo/rocker-org/shiny/issues/92</a></li>
<li><a href="https://stackoverflow.com/questions/30172605/how-do-i-get-into-a-docker-containers-shell">https://stackoverflow.com/questions/30172605/how-do-i-get-into-a-docker-containers-shell</a></li>
</ul>
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