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HTML
125 lines
6.6 KiB
HTML
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<title>Troubleshooting | cellxgene</title>
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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">Installation</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"><b>Troubleshooting</b></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="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="troubleshooting-tips--tricks">Troubleshooting tips & tricks</h1>
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<h4 id="i-tried-to-pip-install-cellxgene-and-got-a-weird-error-i-dont-understand">I tried to <code class="highlighter-rouge">pip install cellxgene</code> and got a weird error I don’t understand</h4>
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<p>This may happen, especially as we work out bugs in our installation process! Please create a new <a href="https://github.com/chanzuckerberg/cellxgene/issues">Github issue</a>, explain what you did, and include all the error messages you saw. It’d also be super helpful if you call <code class="highlighter-rouge">pip freeze</code> and include the full output alongside your issue.</p>
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<h4 id="i-have-a-big-dataset-how-can-i-make-cellxgene-run-as-fast-as-possible">I have a BIG dataset, how can I make cellxgene run as fast as possible?</h4>
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<p>If your dataset requires gigabytes of disk space, you may need to select an appropriate storage format in order to effectively utilize <code class="highlighter-rouge">cellxgene</code>. Tips and tricks:</p>
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<ul>
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<li><code class="highlighter-rouge">cellxgene</code> is optimized for columnar data access. For large datasets, format the expression matrix (<code class="highlighter-rouge">.X</code>) as either a <a href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csc_matrix.html">SciPy CSC sparse matrix</a> or a dense Numpy array (whichever creates a smaller <code class="highlighter-rouge">h5ad</code> file). If you are using <code class="highlighter-rouge">cellxgene prepare</code>, include the <code class="highlighter-rouge">--sparse</code> flag to ensure <code class="highlighter-rouge">.X</code> is formatted as a CSC sparse matrix (by default, <code class="highlighter-rouge">.X</code> will be a dense matrix).</li>
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<li>By default, <code class="highlighter-rouge">cellxgene</code> loads the dataset into memory, and start time is directly proportional to <code class="highlighter-rouge">h5ad</code> file size and the speed of your file system. Expect that large (e.g., million cell) datasets will take minutes to load, even on relatively fast computers with a high performance local hard drive. Once loaded, exploring metadata should still be quick. If this start time is a problem, try the <code class="highlighter-rouge">--backed</code> flag, which will attempt to lazily load data as needed (caveat: subsequent data access may be slower).</li>
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<li>If your dataset size exceeds the size of memory (RAM) on the host computer, differential expression calculations will be extremely slow (or fail, if you run out of virtual memory). In this case, we recommend running with the <code class="highlighter-rouge">--disable-diffexp</code> flag. For datasets that are extremely large, you may also find the <code class="highlighter-rouge">--backed</code> flag improves your ability to explore them.</li>
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</ul>
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<h4 id="im-following-the-developer-instructions-and-get-an-error-about-missing-files-and-directories-when-trying-to-build-the-client">I’m following the developer instructions and get an error about “missing files and directories” when trying to build the client</h4>
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<p>This is likely because you do not have node and npm installed, we recommend using <a href="https://github.com/creationix/nvm">nvm</a> if you’re new to using these tools.</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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