1228 lines
35 KiB
HTML
1228 lines
35 KiB
HTML
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<title>Installation - RAPIDS</title>
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RAPIDS
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Installation
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Initializing search
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<div class="md-header-nav__source">
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<a href="https://github.com/carissalow/rapids/" title="Go to repository" class="md-source">
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<div class="md-source__repository">
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carissalow/rapids
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</a>
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</nav>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M19 18.31V20a2 2 0 01-2 2H7a2 2 0 01-2-2v-3.7c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V12.3c-.46-.18-1.05-.3-2-.3a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V8.3C4.54 8.12 3.95 8 3 8a1 1 0 01-1-1 1 1 0 011-1c.82 0 1.47.08 2 .21V4a2 2 0 012-2h10a2 2 0 012 2v2.16c1.78.31 2.54.97 2.71 1.13.39.39.39 1.03 0 1.42-.39.39-.91.38-1.42 0 0 0-1.04-.71-3.29-.71-1.26 0-2.09.41-3.05.9-1.04.51-2.21 1.1-3.95 1.1-.36 0-.69 0-1-.04V7.95c.3.05.63.05 1 .05 1.26 0 2.09-.41 3.05-.89C14.09 6.59 15.27 6 17 6V4H7v16h10v-2c1.5 0 1.97.29 2 .31M17 10c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 11.08 20.25 10 17 10m0 4c-1.73 0-2.91.59-3.95 1.11-.96.48-1.79.89-3.05.89-.37 0-.7 0-1-.05v2.01c.31.04.64.04 1 .04 1.74 0 2.91-.59 3.95-1.1.96-.48 1.79-.9 3.05-.9 2.25 0 3.29.71 3.29.71.51.39 1.03.39 1.42 0 .39-.39.39-1.02 0-1.42C21.5 15.08 20.25 14 17 14z"/></svg>
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RAPIDS
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carissalow/rapids
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Installation
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Configuration
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Minimal
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<li class="md-nav__item">
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<a href="../../workflow-examples/analysis/" class="md-nav__link">
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Analysis
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Introduction
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<h1 id="installation">Installation<a class="headerlink" href="#installation" title="Permanent link">¶</a></h1>
|
|
<p>You can install RAPIDS using Docker (the fastest), or native instructions for MacOS and Ubuntu</p>
|
|
<div class="tabbed-set" data-tabs="1:3"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><label for="__tabbed_1_1">Docker</label><div class="tabbed-content">
|
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<ol>
|
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<li>
|
|
<p>Install <a href="https://docs.docker.com/desktop/">Docker</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Pull our RAPIDS container
|
|
<div class="highlight"><pre><span></span><code>docker pull agamk/rapids:latest<span class="sb">`</span>
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Run RAPIDS' container (after this step is done you should see a
|
|
prompt in the main RAPIDS folder with its python environment active)</p>
|
|
<div class="highlight"><pre><span></span><code>docker run -it agamk/rapids:latest
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Pull the latest version of RAPIDS</p>
|
|
<div class="highlight"><pre><span></span><code>git pull
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p><em>Optional</em>. You can edit RAPIDS files with <code>vim</code> but we recommend using <code>Visual Studio Code</code> and its <code>Remote Containers</code> extension</p>
|
|
<details class="info"><summary>How to configure Remote Containers extension</summary><ul>
|
|
<li>Make sure RAPIDS container is running<ul>
|
|
<li>Install the <a href="https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers">Remote - Containers extension</a></li>
|
|
<li>Go to the <code>Remote Explorer</code> panel on the left hand sidebar</li>
|
|
<li>On the top right dropdown menu choose <code>Containers</code></li>
|
|
<li>Double click on the <code>agamk/rapids</code> container in the<code>CONTAINERS</code> tree</li>
|
|
<li>A new VS Code session should open on RAPIDS main folder insidethe container.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</details>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
<input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><label for="__tabbed_1_2">MacOS</label><div class="tabbed-content">
|
|
<p>We tested these instructions in Catalina</p>
|
|
<ol>
|
|
<li>
|
|
<p>Install <a href="https://brew.sh/">brew</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Install MySQL</p>
|
|
<div class="highlight"><pre><span></span><code>brew install mysql
|
|
brew services start mysql
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R 4.0, pandoc and rmarkdown. If you have other instances of R, we recommend uninstalling them</p>
|
|
<div class="highlight"><pre><span></span><code>brew install r
|
|
brew install pandoc
|
|
Rscript --vanilla -e <span class="s1">'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install miniconda (restart your terminal afterwards)</p>
|
|
<div class="highlight"><pre><span></span><code>brew cask install miniconda
|
|
conda init zsh <span class="c1"># (or conda init bash)</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Clone our repo</p>
|
|
<div class="highlight"><pre><span></span><code>git clone https://github.com/carissalow/rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Create a python virtual environment</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nb">cd</span> rapids
|
|
conda env create -f environment.yml -n rapids
|
|
conda activate rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R packages and virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code>snakemake -j1 renv_install
|
|
snakemake -j1 renv_restore
|
|
</code></pre></div>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note<p>This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.</p>
|
|
</p>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
|
|
</li>
|
|
</ol>
|
|
</div>
|
|
<input id="__tabbed_1_3" name="__tabbed_1" type="radio" /><label for="__tabbed_1_3">Ubuntu</label><div class="tabbed-content">
|
|
<p>We tested on Ubuntu 18.04 & 20.04</p>
|
|
<ol>
|
|
<li>
|
|
<p>Install dependencies</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install libcurl4-openssl-dev
|
|
sudo apt install libssl-dev
|
|
sudo apt install libxml2-dev
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install MySQL</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install libmysqlclient-dev
|
|
sudo apt install mysql-server
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Add key for R’s repository.</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Add R’s repository</p>
|
|
<ol>
|
|
<li>
|
|
<p>For 18.04 <br />
|
|
<div class="highlight"><pre><span></span><code>sudo add-apt-repository <span class="s1">'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'</span>
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>For 20.04
|
|
<div class="highlight"><pre><span></span><code>sudo add-apt-repository <span class="s1">'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'</span>
|
|
</code></pre></div></p>
|
|
</li>
|
|
</ol>
|
|
</li>
|
|
<li>
|
|
<p>Install R 4.0. If you have other instances of R, we recommend uninstalling them</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt update
|
|
sudo apt install r-base
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install Pandoc and rmarkdown</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install pandoc
|
|
Rscript --vanilla -e <span class="s1">'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'</span>
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install git</p>
|
|
<div class="highlight"><pre><span></span><code>sudo apt install git
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install <a href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html">miniconda</a></p>
|
|
</li>
|
|
<li>
|
|
<p>Restart your current shell</p>
|
|
</li>
|
|
<li>
|
|
<p>Clone our repo:</p>
|
|
<div class="highlight"><pre><span></span><code>git clone https://github.com/carissalow/rapids
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Create a python virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nb">cd</span> rapids
|
|
conda env create -f environment.yml -n MY_ENV_NAME
|
|
conda activate MY_ENV_NAME
|
|
</code></pre></div>
|
|
</li>
|
|
<li>
|
|
<p>Install R packages and virtual environment:</p>
|
|
<div class="highlight"><pre><span></span><code>snakemake -j1 renv_install
|
|
snakemake -j1 renv_restore
|
|
</code></pre></div>
|
|
<div class="admonition note">
|
|
<p class="admonition-title">Note<p>This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.</p>
|
|
</p>
|
|
</div>
|
|
</li>
|
|
<li>
|
|
<p>Make RAPIDS script executable
|
|
<div class="highlight"><pre><span></span><code>chmod +x rapids
|
|
</code></pre></div></p>
|
|
</li>
|
|
<li>
|
|
<p>Check that RAPIDS is working
|
|
<div class="highlight"><pre><span></span><code>./rapids -j1
|
|
</code></pre></div></p>
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</li>
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