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204 lines
8.8 KiB
HTML
204 lines
8.8 KiB
HTML
<!DOCTYPE html>
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<html lang="en-US">
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<head>
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<meta charset="UTF-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>Install | cellxgene</title>
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<meta property="og:title" content="Install" />
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<meta property="og:locale" content="en_US" />
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<meta name="description" content="An interactive explorer for single-cell transcriptomics data" />
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<meta property="og:description" content="An interactive explorer for single-cell transcriptomics data" />
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<link rel="canonical" href="https://chanzuckerberg.github.io/cellxgene/posts/install.html" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/install.html" />
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=4d1a0c6eaf004182077c1e7585470f6009e3283a">
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<!--[if lt IE 9]>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
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<![endif]-->
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</head>
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<body>
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<div class="wrapper">
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<header>
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<img src="/cellxgene/cellxgene-logo.png" alt="cellxgene" />
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<p>An interactive explorer for single-cell transcriptomics data</p>
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<p>
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<a href="/cellxgene/" class="btn">Quick start</a><br>
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<a href="/cellxgene/posts/install" class="btn"><b>Installation</b></a><br>
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<a href="/cellxgene/posts/gallery" class="btn">Gallery</a><br>
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<a href="/cellxgene/posts/demo-data" class="btn">Demo datasets</a><br>
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<a href="/cellxgene/posts/prepare" class="btn">Preparing your data</a><br>
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<a href="/cellxgene/posts/launch" class="btn">Launching cellxgene</a><br>
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<a href="/cellxgene/posts/hosted" class="btn">Hosting cellxgene</a><br>
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<a href="/cellxgene/posts/annotations" class="btn">Annotating data</a><br>
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<a href="/cellxgene/posts/methods" class="btn">Methods</a><br>
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<a href="/cellxgene/posts/troubleshooting" class="btn">Troubleshooting</a><br>
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<a href="/cellxgene/posts/roadmap" class="btn">Roadmap</a><br>
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<a href="/cellxgene/posts/contribute" class="btn">Contributing (ideas or code)</a><br>
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<a href="/cellxgene/posts/contact" class="btn">Contact & finding help</a><br>
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<a href="/cellxgene/posts/cellxgene_cziscience_com" class="btn">cellxgene.cziscience.com</a><br>
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<a href="https://github.com/chanzuckerberg/cellxgene" class="btn" target="_blank">Code</a>
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</p>
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</header>
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<section>
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<h1 id="installing-cellxgene">Installing cellxgene</h1>
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<p>Cellxgene has two parts:</p>
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<ul>
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<li><a href="launch"><code class="language-plaintext highlighter-rouge">cellxgene</code></a> is the main explorer application, which takes an already-processed <code class="language-plaintext highlighter-rouge">h5ad</code> file as input. This is installed by default.</li>
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<li><a href="prepare"><code class="language-plaintext highlighter-rouge">cellxgene prepare</code></a> provides auxiliary functionality for preparing your dataset. This is <em>not</em> installed by default.</li>
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</ul>
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<h2 id="requirements">Requirements</h2>
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<p>You’ll need <strong>python 3.6+</strong> and an up-to-date version of <strong>Google Chrome</strong>.
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The web UI is tested on OSX and Windows using Chrome, and the python CLI is tested on OSX and Ubuntu (via WSL/Windows).
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It should work on other platforms, but if you run into trouble let us know.</p>
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<p><a href="https://www.python.org/downloads/">Python.org</a> has help on installing a recent
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version of Python, including the pip package manager. Chrome is available at
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<a href="https://google.com/chrome">Google.com/chrome</a>.</p>
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<h2 id="basic-install-using-pip">Basic install using pip</h2>
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<p>To install the <code class="language-plaintext highlighter-rouge">cellxgene</code> explorer alone, run:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene
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</code></pre></div></div>
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<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> and the optional <code class="language-plaintext highlighter-rouge">cellxgene prepare</code>, run:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene[prepare]
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</code></pre></div></div>
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<p><em>Note: if the aforementioned optional <code class="language-plaintext highlighter-rouge">prepare</code> package installation fails, you can also install these packages directly:</em></p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install scanpy>=1.3.7 python-igraph louvain>=0.6
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</code></pre></div></div>
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<p><em>On various Linux platforms, you may also need to install build dependencies first:</em></p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>sudo apt-get install build-essential python-dev
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pip install scanpy>=1.3.7 python-igraph louvain>=0.6
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</code></pre></div></div>
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<p>If you already have <code class="language-plaintext highlighter-rouge">cellxgene</code> installed, you can update to the most recent version by running:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene --upgrade
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</code></pre></div></div>
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<h2 id="using-a-conda-environment">Using a conda environment</h2>
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<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> alone, run:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>conda create --yes -n cellxgene python=3.7
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conda activate cellxgene
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pip install cellxgene
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</code></pre></div></div>
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<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> and the optional <code class="language-plaintext highlighter-rouge">cellxgene prepare</code>, run:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>conda create --yes -n cellxgene python=3.7
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conda activate cellxgene
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pip install cellxgene[prepare]
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</code></pre></div></div>
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<h2 id="using-a-virtual-environment">Using a virtual environment</h2>
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<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> alone, run:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ENV_NAME=cellxgene
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python3.7 -m venv ${ENV_NAME}
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source ${ENV_NAME}/bin/activate
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pip install cellxgene
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</code></pre></div></div>
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<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> and <code class="language-plaintext highlighter-rouge">cellxgene prepare</code>, run:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ENV_NAME=cellxgene
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python3.7 -m venv ${ENV_NAME}
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source ${ENV_NAME}/bin/activate
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pip install cellxgene[prepare]
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</code></pre></div></div>
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<h2 id="using-docker">Using docker</h2>
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<p>Build the image</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker build . -t cellxgene
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</code></pre></div></div>
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<p>Run the container and mount data (change data location, <code class="language-plaintext highlighter-rouge">--port</code> and <code class="language-plaintext highlighter-rouge">--host</code> parameters as needed)</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker run -v "$PWD/example-dataset/:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad
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</code></pre></div></div>
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<p>You will need to use <code class="language-plaintext highlighter-rouge">--host 0.0.0.0</code> to have the container listen to incoming requests from the browser</p>
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</section>
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<footer>
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<p>This project is maintained by <a href="https://github.com/chanzuckerberg">chanzuckerberg</a></p>
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</footer>
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</div>
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<script src="/cellxgene/assets/js/scale.fix.js"></script>
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</body>
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</html>
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