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cziscience landing page (#1347)

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* fix dead link in launch page

* first cut at landing page

* wording changes

* add additional refinements

* fixes from PR review
This commit is contained in:
Bruce Martin
2020-04-03 16:30:02 -07:00
committed by GitHub
parent de8033e551
commit 0d9f24115c
25 changed files with 446 additions and 260 deletions
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docs/_site/posts/install.html
+29 -25
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@@ -16,10 +16,10 @@
<meta property="og:url" content="http://localhost:4000/cellxgene/posts/install.html" />
<meta property="og:site_name" content="cellxgene" />
<script type="application/ld+json">
{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","url":"http://localhost:4000/cellxgene/posts/install.html","headline":"Install","@context":"http://schema.org"}</script>
{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Install","url":"http://localhost:4000/cellxgene/posts/install.html","@context":"http://schema.org"}</script>
<!-- End Jekyll SEO tag -->
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=d2171b9a2f9935b8b92c3103c93405d1d74ef2b3">
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=88411ae4b44d899609d211ed2db5c41e4fba3068">
<!--[if lt IE 9]>
<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
<![endif]-->
@@ -85,6 +85,10 @@
<a href="/cellxgene/posts/contact" class="btn">Contact & finding help</a><br>
<a href="/cellxgene/posts/cellxgene_cziscience_com" class="btn">cellxgene.cziscience.com</a><br>
<a href="https://github.com/chanzuckerberg/cellxgene" class="btn" target="_blank">Code</a>
</p>
@@ -96,8 +100,8 @@
<p>Cellxgene has two parts:</p>
<ul>
<li><a href="launch"><code class="highlighter-rouge">cellxgene</code></a> is the main explorer application, which takes an already-processed <code class="highlighter-rouge">h5ad</code> file as input. This is installed by default.</li>
<li><a href="prepare"><code class="highlighter-rouge">cellxgene prepare</code></a> provides auxiliary functionality for preparing your dataset. This is <em>not</em> installed by default.</li>
<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>
<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>
</ul>
<h2 id="requirements">Requirements</h2>
@@ -112,61 +116,61 @@ version of Python, including the pip package manager. Chrome is available at
<h2 id="basic-install-using-pip">Basic install using pip</h2>
<p>To install the <code class="highlighter-rouge">cellxgene</code> explorer alone, run:</p>
<p>To install the <code class="language-plaintext highlighter-rouge">cellxgene</code> explorer alone, run:</p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene
</code></pre></div></div>
<p>To install <code class="highlighter-rouge">cellxgene</code> and the optional <code class="highlighter-rouge">cellxgene prepare</code>, run:</p>
<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>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene[prepare]
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene[prepare]
</code></pre></div></div>
<p><em>Note: if the aforementioned optional <code class="highlighter-rouge">prepare</code> package installation fails, you can also install these packages directly:</em></p>
<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>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install scanpy&gt;=1.3.7 python-igraph louvain&gt;=0.6
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install scanpy&gt;=1.3.7 python-igraph louvain&gt;=0.6
</code></pre></div></div>
<p><em>On various Linux platforms, you may also need to install build dependencies first:</em></p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>sudo apt-get install build-essential python-dev
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>sudo apt-get install build-essential python-dev
pip install scanpy&gt;=1.3.7 python-igraph louvain&gt;=0.6
</code></pre></div></div>
<p>If you already have <code class="highlighter-rouge">cellxgene</code> installed, you can update to the most recent version by running:</p>
<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>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene --upgrade
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene --upgrade
</code></pre></div></div>
<h2 id="using-a-conda-environment">Using a conda environment</h2>
<p>To install <code class="highlighter-rouge">cellxgene</code> alone, run:</p>
<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> alone, run:</p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>conda create --yes -n cellxgene python=3.7
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>conda create --yes -n cellxgene python=3.7
conda activate cellxgene
pip install cellxgene
</code></pre></div></div>
<p>To install <code class="highlighter-rouge">cellxgene</code> and the optional <code class="highlighter-rouge">cellxgene prepare</code>, run:</p>
<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>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>conda create --yes -n cellxgene python=3.7
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>conda create --yes -n cellxgene python=3.7
conda activate cellxgene
pip install cellxgene[prepare]
</code></pre></div></div>
<h2 id="using-a-virtual-environment">Using a virtual environment</h2>
<p>To install <code class="highlighter-rouge">cellxgene</code> alone, run:</p>
<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> alone, run:</p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ENV_NAME=cellxgene
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ENV_NAME=cellxgene
python3.7 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
pip install cellxgene
</code></pre></div></div>
<p>To install <code class="highlighter-rouge">cellxgene</code> and <code class="highlighter-rouge">cellxgene prepare</code>, run:</p>
<p>To install <code class="language-plaintext highlighter-rouge">cellxgene</code> and <code class="language-plaintext highlighter-rouge">cellxgene prepare</code>, run:</p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ENV_NAME=cellxgene
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>ENV_NAME=cellxgene
python3.7 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
pip install cellxgene[prepare]
@@ -176,15 +180,15 @@ pip install cellxgene[prepare]
<p>Build the image</p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker build . -t cellxgene
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker build . -t cellxgene
</code></pre></div></div>
<p>Run the container and mount data (change data location, <code class="highlighter-rouge">--port</code> and <code class="highlighter-rouge">--host</code> parameters as needed)</p>
<p>Run the container and mount data (change data location, <code class="language-plaintext highlighter-rouge">--port</code> and <code class="language-plaintext highlighter-rouge">--host</code> parameters as needed)</p>
<div class="highlighter-rouge"><div class="highlight"><pre class="highlight"><code>docker run -v "$PWD/example-dataset/:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad
<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
</code></pre></div></div>
<p>You will need to use <code class="highlighter-rouge">--host 0.0.0.0</code> to have the container listen to incoming requests from the browser</p>
<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>
</section>
<footer>