https://docs.uabgrid.uab.edu/w/index.php?action=history&feed=atom&title=QIIME_2 2026-06-02T05:36:22Z Revision history for this page on the wiki MediaWiki 1.38.2 https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_2&diff=6171&oldid=prev 2021-05-28T15:46:09Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:46, 28 May 2021</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24">Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/pre&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/pre&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>== Jupyter Notebook support(optional) ==</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== Jupyter Notebook support (optional) ==</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>By default, the Jupyter Notebook running on the OnDemand portal is from a basic installation of Jupyter Notebook which doesn't have the ability to do QIIME 2 visualization. You will need to perform these additional steps to make it work.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>By default, the Jupyter Notebook running on the OnDemand portal is from a basic installation of Jupyter Notebook which doesn't have the ability to do QIIME 2 visualization. You will need to perform these additional steps to make it work.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr> </table>

Louistw@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_2&diff=6170&oldid=prev 2021-05-27T22:18:05Z

<p>Add QIIME 2 installation guide</p> <p><b>New page</b></p><div>__TOC__<br /> <br /> = About =<br /> QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.<br /> <br /> = Install =<br /> Since QIIME 2 updates frequently. It's easier to maintain your own QIIME 2 installation, and update as needed. Here we suggest using [[Anaconda]] to manage your instances. If you have never used Anaconda before, please refer to [[Anaconda]].<br /> <br /> Once you have [[Anaconda]] setup, please follow the following steps to install your own copy of QIIME 2.<br /> <br /> &lt;pre&gt;<br /> # Load Anaconda module<br /> module load Anaconda3<br /> <br /> # Download the conda environment file for QIIME 2<br /> wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml<br /> <br /> # Use the downloaded conda environment file to install QIIME 2<br /> # And named it: qiime2-2021.4<br /> conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml<br /> <br /> # Remove the conda environment file after installation<br /> rm qiime2-2021.4-py38-linux-conda.yml<br /> &lt;/pre&gt;<br /> <br /> == Jupyter Notebook support(optional) ==<br /> By default, the Jupyter Notebook running on the OnDemand portal is from a basic installation of Jupyter Notebook which doesn't have the ability to do QIIME 2 visualization. You will need to perform these additional steps to make it work.<br /> <br /> &lt;pre&gt;<br /> # Load Anaconda module<br /> module load Anaconda3<br /> <br /> # Activate the QIIME 2 environment we just installed<br /> conda activate qiime2-2021.4<br /> <br /> # Install required package<br /> conda install -y nb_conda<br /> <br /> # Enable the extension<br /> jupyter serverextension enable --py qiime2<br /> &lt;/pre&gt;<br /> <br /> Now, you can go to [https://rc.uab.edu/pun/sys/dashboard/batch_connect/sys/jupyter/session_contexts/new the interactive job] to start Jupyter Notebook, put this line in the Environment Setup box to enable the conda environment you just installed:<br /> <br /> &lt;pre&gt;<br /> conda activate qiime2-2021.4<br /> &lt;/pre&gt;</div>

Louistw@uab.edu