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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
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<title>Pre-course</title>
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<body class="fullcontent">
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<div class="quarto-title">
<h1 class="title">Pre-course</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="registration-on-scilifelab-serve" class="level4">
<h4 class="anchored" data-anchor-id="registration-on-scilifelab-serve"><img border="0" src="https://www.svgrepo.com/show/529862/server-path.svg" width="15" height="15"> Registration on SciLifeLab Serve</h4>
<hr>
<p>In order to be able to access the lab notebooks for this course you need to have access to <a href="https://serve.scilifelab.se">SciLifeLab Serve</a>.</p>
<p>Please register with your university email address. In the registration form there is a field called “Do you require support?”, in here please write that you are registering to take part in the course OMICSINT_H24. Do not forget to also confirm your e-mail address by clicking on a link in the activation email. This needs to be done before Friday October 11 so that the SciLifeLab Serve admins can set up your account in the way that is required by the course.</p>
<p>For lunching practicals please follow the instructions <a href="./session_intro/Instructions%20for%20course%20OMICSINT_H24.pdf">here</a>.</p>
</section>
<section id="preparation-for-the-tutorial" class="level4">
<h4 class="anchored" data-anchor-id="preparation-for-the-tutorial"><img border="0" src="https://www.svgrepo.com/show/26916/book.svg" width="15" height="15"> Preparation for the tutorial</h4>
<hr>
<p>This workshop will comprise both lectures and hands-on exercises. While you will be able to follow all exercises from the html files, we recommend that you prepare by</p>
<ol type="1">
<li><a href="#programming-with-r-and-python">Familiarizing yourself with basic R and Python</a></li>
<li><a href="#docker-instructions">Installing the containers</a>.</li>
</ol>
<p>If you are interested you can go through the <a href="reading_materials.html">additional reading materials</a>.</p>
</section>
<section id="programming-with-r-and-python" class="level4">
<h4 class="anchored" data-anchor-id="programming-with-r-and-python"><img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="25" height="25"> Programming with R and Python</h4>
<hr>
<p>The course will be taught using both R and Python depending on the tools available. While you will be able to follow all lectures and exercises conceptually, it is helpful if you are familiar with basic usage of both programming languages:</p>
<ul>
<li><a href="https://swcarpentry.github.io/r-novice-inflammation/">R (part_1)</a></li>
<li><a href="http://swcarpentry.github.io/r-novice-gapminder/">R (part_2)</a></li>
<li><a href="https://swcarpentry.github.io/python-novice-inflammation/">Python (part_1)</a></li>
<li><a href="http://swcarpentry.github.io/python-novice-gapminder/">Python (part_2)</a></li>
</ul>
<p>You should also be familiar with basic command line input (<code>mkdir</code>, <code>cd</code>, <code>ls</code>, <code>cp</code>, <code>mv</code>).</p>
</section>
<section id="docker-instructions" class="level4">
<h4 class="anchored" data-anchor-id="docker-instructions"><img border="0" src="https://www.svgrepo.com/show/303231/docker-logo.svg" width="25" height="25"> Docker instructions</h4>
<hr>
<p>We have currently ran different tests and evaluations to make sure SciLifeLab Serve is roboust and functional during the course time. However, as a back up plan for running the notebooks in case that SciLifeLab Serve service was lagging, we have prepared docker images for different labs with all the necessary software installed. You can follow the instructions below to install the docker and run the notebooks locally.</p>
<ul>
<li><a href="https://docs.docker.com/get-docker/">Install Docker</a></li>
<li><a href="https://git-scm.com/book/en/v2/Getting-Started-Installing-Git">Install git</a> (optional)</li>
<li><a href="https://github.com/NBISweden/workshop_omics_integration/tree/OMICSINT_H24">Clone the Github repository for the course</a> (optional)</li>
</ul>
<section id="pull-docker-images" class="level5">
<h5 class="anchored" data-anchor-id="pull-docker-images">Pull docker images</h5>
<p>At this point you need to create the two containers for all Rstudio or Jupyter notebooks. In a directory containing the unzip folder <code>workshop_omics_integration/</code>, create the containers by either:</p>
<details>
<summary>
<strong>> Download image from Dockerhub</strong>
</summary>
<p>Select the approprtiate lab from <a href="https://hub.docker.com/repository/docker/rasoolsnbis/omicsint_h24/tags">dockerhub repo</a>, pull and run the images.</p>
<pre><code> ########### For example for GSA and UMAP labs ###########
# cd to your desired directory
docker pull rasoolsnbis/omicsint_h24:session_gsa_amd_v.h24.a1ae0fc
docker pull rasoolsnbis/omicsint_h24:session_ml_umap_data_integration_amd_v.h24.6d635ce
# for Jupyter lab use the following command
docker run --rm --platform=linux/amd64 -d -p 8888:8888/tcp rasoolsnbis/omicsint_h24:session_ml_umap_data_integration_amd_v.h24.6d635ce
# for Rstudio lab use the following command
docker run --rm --platform=linux/amd64 -d -p 8787:8787/tcp rasoolsnbis/omicsint_h24:session_gsa_amd_v.h24.a1ae0fc</code></pre>
</details>
</section>
<section id="mounting-a-local-folder-to-a-docker-container" class="level5">
<h5 class="anchored" data-anchor-id="mounting-a-local-folder-to-a-docker-container">Mounting a Local Folder to a Docker Container</h5>
<p>To mount a local folder to a Docker container when running it, use the <code>-v</code> (or <code>--volume</code>) option in the <code>docker run</code> command. The syntax is:</p>
<p>For example, if you want to mount a local folder, such as <code>/home/user/my_data</code>, to a directory inside the container, say <code>/app/data</code>, the <code>docker run</code> command would look like this:</p>
<pre><code>docker run --rm --platform=linux/amd64 -d -p 8888:8888/tcp \
-v /home/user/my_data:/app/data \
rasoolsnbis/omicsint_h24:session_ml_umap_data_integration_amd_v.h24.6d635ce</code></pre>
<p>In this example:</p>
<p><code>/home/user/my_data</code>: The local folder on your host machine. <code>/app/data</code>: The directory inside the Docker container where the local folder will be mounted. Any files in the local folder will be accessible in the specified directory inside the container, and any changes made inside the container will be reflected in your local folder.</p>
</section>
<section id="launch-rstudio-or-jupyter" class="level5">
<h5 class="anchored" data-anchor-id="launch-rstudio-or-jupyter">Launch RStudio or Jupyter</h5>
<p>Ensure you have followed all the instructions above and that your containers are running. If you have followed the instructions, you can simply access either RStudio or Jupyter from your browser with: - <code>localhost:8888</code> to launch jupyter - <code>localhost:8787</code> to launch rstudio</p>
<p>If you want to verify that your containers are running use <code>docker ps</code>.</p>
</section>
<section id="stop-the-containers" class="level5">
<h5 class="anchored" data-anchor-id="stop-the-containers">Stop the containers</h5>
<p>To stop the containers write <code>docker stop [container name]</code>.</p>
<p><a href="https://nbisweden.github.io/workshop_omics_integration/">Back to Homepage</a></p>
</section>
</section>
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