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<!DOCTYPE html>
<html lang="en">
<head>
<meta name="generator" content=
"HTML Tidy for HTML5 (experimental) for Mac OS X https://github.com/w3c/tidy-html5/tree/c63cc39">
<meta charset="utf-8">
<title>Easy deployment of tools with complex dependencies using
Docker and Galaxy on the Cloud</title>
<meta name="description" content=
"VLSCI Summer Internship 2014/15 Final Presentation">
<meta name="author" content="Simon Belluzzo">
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content=
"black-translucent">
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</head>
<body>
<div class="reveal">
<div class="slides">
<section id="title-slide">
<h3>Easy Deployment of Tools with Complex Dependencies
using Docker and Galaxy on the Cloud</h3>
<div><img class="title-img" height="200" data-src=
"images/galaxyLogo.png" alt="Galaxy Logo"> + <img class=
"title-img" height="200" data-src=
"images/docker_large_v-dark-trans.png" alt="Docker Logo"> =
<img class="title-img" height="200" data-src=
"images/happy-ira.jpg" alt="Happy Ira"></div>
<h4>Simon Belluzzo - Ira Cooke</h4><a href=
"http://simon.belluzzo.id.au/vlsci-intern-slides">http://simon.belluzzo.id.au/vlsci-intern-slides</a>
<img id="happy-arrow" class="fragment" height="200"
data-src="images/happyira.svg" alt=
"Arrow pointing at a happy Ira">
</section>
<section>
<h3>Galaxy for the Uninitiated</h3>
</section>
<section>
<div class="stretch">
<img class="naked" data-src=
"images/galaxyLaunchWorkflow.png" alt=
"Galaxy executing a workflow">
<div style="font-size: smaller;">
<a href="https://usegalaxy.org">Galaxy Main</a> -
<a href="https://genome.edu.au/wiki/GVL">GVL</a> -
<a href="http://galaxyproject.org">Galaxy Project</a>
</div>
</div>
<aside class="notes"></aside>
</section>
<section>
<h3>Tool Dependency Asteroid Fields</h3>
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<aside class="notes"></aside>
</section>
<section>
<h3>Containers & Docker</h3>
</section>
<section>
<h3>Containers</h3><img src="images/contvsvm.png" style=
"background: #fff" alt="VMs vs Containers">
<ul style="font-size: smaller;">
<li class="fragment">Other than the kernel, containers
are isolated from each other and the host</li>
<li class="fragment">Sit in between chroot and full
virtualization</li>
</ul>
<aside class="notes"></aside>
</section>
<section>
<h3>And Docker..?</h3>
<ul>
<li class="fragment">Convenience wrapper around container
management</li>
<li class="fragment">Mixes in Git/DVCS ideas in dealing
with image changes/layers</li>
<li class="fragment">Docker Hub provides hosting and
automated building</li>
<li class="fragment"><strong>For us:</strong> Enhances
accessibility and reproducibility</li>
</ul>
<p class="fragment">Docker is not the only player, expect
competition</p>
<aside class="notes"></aside>
</section>
<section>
<h3>Project Aims</h3>
<ol>
<li class="fragment">Create a ProtK Docker image</li>
<li class="fragment">Adapt Galaxy wrappers to use the
image</li>
<li class="fragment">Test deployment and execution on
standalone and cloud Galaxy instances (for use with
GVL)</li>
</ol>
</section>
<section>
<h3>Docker Image Building</h3>
<aside class="notes">
Balancing automated builds, size, clarity,
reproducibility and maintainability, build tools
separate, nested builds, size C++ std changes, boost
conflicts, required ruby versions
</aside>
</section>
<section id="build-slide">
<img class="naked" data-src="images/dockerfile.svg" style=
"vertical-align: top; display: inline-block; width: 49%;"
alt="ProtK Dockerfile (abridged)"> <img class=
"fragment naked" data-src="images/image_building.svg"
style="vertical-align: top; display: inline-block; width: 49%;"
alt="Automated builds are triggered by pushing code">
</section>
<section>
<h3>Galaxy Integration</h3>
<aside class="notes">
Rapidly evolving, one or two extra tags in job conf,
wrappers and fallbacks, wrapper scripts and runtimes Test
cases and tutorial run throughs
</aside>
</section>
<section>
<img class="naked" data-src="images/galaxy_local.svg" alt=
"Installing from the Galaxy Tool Shed; with and without Docker">
<div style="font-size: smaller;">
<ul style="list-style-type: none">
<li class="fragment">Without Docker:</li>
<li>
<ul>
<li class="fragment">The "admin" may not have the
required expertise for installation</li>
<li class="fragment">Installation steps can differ
significantly across operating systems</li>
<li class="fragment">Documentation can be patchy or
non-existent</li>
</ul>
</li>
<li class="fragment">With Docker:</li>
<li>
<ul>
<li class="fragment">Graceful fallback</li>
<li class="fragment">Backwards-compatible with
non-Dockerised tools</li>
<li class="fragment">Consistent method to install
tools</li>
</ul>
</li>
</ul>
</div>
</section>
<section>
<h3>GVL/Galaxy on the Cloud Integration</h3>
<ul>
<li class="fragment">Dockerised tools run fine on either
master or worker nodes (with the usual scaling abilities)</li>
<li class="fragment">Not compatible with the current GVL
(new GVL version will be compatible)</li>
<li class="fragment">Don't have to wait; You can use our
custom Galaxy on the Cloud image & bucket (NeCTAR
only currently)</li>
<ul>
<li class="fragment">Launchable by GVL Launcher
(with custom settings) or by CLI tool</li>
<li class="fragment">
<a href="http://simon.belluzzo.id.au/cloudman-docker-guide">
Quickstart Guide available
</a>
</li>
</ul>
</ul>
<aside class="notes">
Issues with GVL instances due to old kernel, and SGE
conflict. Built own 'GVL-lite'/Galaxy in the Cloud.
Documentation lacking/inaccurate Works fine with SLURM,
both locally and on CM worker nodes CLI script to start
up a cluster on any region, or can use GVL launcher with
the right options Issues with multiple processes, unaware
of updates Automated Selenium testcases and runthroughs
</aside>
</section>
<section>
<h3>Advantages</h3>
<ul>
<li class="fragment">Transparent to end-user</li>
<li class="fragment">Simple to deploy & update</li>
<li class="fragment">Aids reproducibility</li>
<li class="fragment">Isolates tools and their
dependencies from each other and the host operating
system</li>
</ul>
</section>
<section>
<h3>Disadvantages</h3>
<ul>
<li class="fragment">Some Docker bugs (transient, and
fixed in new versions)</li>
<li class="fragment">Duplication of dependencies &
large image sizes</li>
<li class="fragment">Nascent tech, patterns and best
practices still forming</li>
<li class="fragment">Docker, Inc uncertainty</li>
<li class="fragment"><strong><u>Security</u></strong> (at
least in Galaxy's use of Docker)</li>
</ul>
</section>
<section>
<h3>Further Work</h3>
<ul>
<li class="fragment">Inclusion of a Docker registry
mirror</li>
<li class="fragment">Enhanced Galaxy-Docker integration
<ul>
<li>Allowing use of multiple containers in a single
wrapper</li>
<li>Container sharing between tools</li>
</ul>
</li>
<li class="fragment">Docker image and container
management options</li>
<li class="fragment">Better image build process
(Dockerfile or otherwise)</li>
<li class="fragment">Wine in Docker for Windows-based
tools</li>
</ul>
<aside class="notes"></aside>
</section>
<section id="ack-slide">
<div>
<h4>Acknowledgements</h4>
<div class="acknowledge">
<ul>
<li>Ira Cooke</li>
<li>Nathan Hall</li>
<li>Andrew Robinson</li>
<li>Nuwan Goonasekera</li>
<li>Christina Hall</li>
<li>
<a href="http://vlsci.org.au">VLSCI</a> LSCC for
funding
</li>
<li>
<a href="http://nectar.org.au">NeCTAR</a> for
infrastructure
</li>
</ul>
</div>
<div class="acknowledge">
OSS projects utilised:
<ul>
<li>
<a href="http://galaxyproject.org">Galaxy</a>
</li>
<li>
<a href=
"https://wiki.galaxyproject.org/CloudMan">CloudMan</a>
</li>
<li>
<a href="https://www.docker.com">Docker</a>
</li>
<li>
<a href="http://www.ansible.com">Ansible</a>
</li>
<li>
<a href="https://www.debian.org">Debian</a>
</li>
<li>
<a href="http://www.ubuntu.com">Ubuntu</a>
</li>
</ul>
</div>
</div>
<div>
<h4>Contact</h4>
<div class="contact">
<img height="80" data-src=
"https://avatars.githubusercontent.com/simonalpha" alt=
"Simon GitHub Profile Pic">
<ul>
<li>
<a href=
"mailto:[email protected]">[email protected]</a>
</li>
<li>@simonalpha</li>
</ul>
</div>
<div class="contact">
<img height="80" data-src=
"https://avatars.githubusercontent.com/iracooke" alt=
"Ira GitHub Profile Pic">
<ul style="margin auto;">
<li>
<a href=
"mailto:[email protected]">[email protected]</a>
</li>
<li>@iracooke</li>
</ul>
</div>
</div><a href=
"http://simon.belluzzo.id.au/vlsci-intern-slides">http://simon.belluzzo.id.au/vlsci-intern-slides</a>
</section>
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