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<p><center></p>
<h1 id="intermediate-advanced-shell-for-bioinformatics"><strong>Intermediate-Advanced Shell for Bioinformatics</strong><a class="headerlink" href="#intermediate-advanced-shell-for-bioinformatics" title="Permanent link">¶</a></h1>
<p></center></p>
<p><br></p>
<p align="center"><img src="images/dna_tux.png" alt="drawing" width="300"/></p>
<p><br></p>
<!--- check -->
<table>
<thead>
<tr>
<th align="left"><strong>Lesson</strong></th>
<th align="left"><strong>Overview</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td align="left">1. <a href="0_introduction/">UNIX,Linux & UNIX Shell</a></td>
<td align="left">Introduction to UNIX operating system, Linux and UNIX Shell</td>
</tr>
<tr>
<td align="left">2. <a href="1_download_data/">Download and verify data</a></td>
<td align="left">Downloading data with <code>wget</code>/<code>curl</code> and check the transferred data’s integrity with check‐sums</td>
</tr>
<tr>
<td align="left">3. <a href="2_unixshellbasics/">UNIX Shell Basics & Recap</a></td>
<td align="left">Navigating Files & Directories and a review of commands used in routine tasks</td>
</tr>
<tr>
<td align="left">4. <a href="4_inspectmanipluate/">Inspecting and Manipulating Text Data with UNIX Tools - Part 1</a></td>
<td align="left">Inspect file/s with utilities such as <code>head</code>,<code>less</code>. Extracting and formatting tabular data. Magical <code>grep</code>. Substitute matching patterns with <code>sed</code></td>
</tr>
<tr>
<td align="left">5. <a href="5_inspectmanipulate2/">Inspecting and Manipulating Text Data with UNIX Tools - Part 2</a></td>
<td align="left">Text processing with <code>awk</code> and <code>bioawk</code></td>
</tr>
<tr>
<td align="left">6. <a href="6_automate_fileprocessing_find_xargs/">Automating File-Processing with find and xargs</a></td>
<td align="left">Search files by pattern with <code>find</code> and use <code>xargs</code> to execute a command for those objects matching the pattern</td>
</tr>
<tr>
<td align="left">7. <a href="puzzles/">Puzzles</a> 🧩</td>
<td align="left">Can you use shell scripts to solve these "real" life challenged in molecular biology ?</td>
</tr>
</tbody>
</table>
<hr />
<h1 id="attribution-notice">Attribution Notice<a class="headerlink" href="#attribution-notice" title="Permanent link">¶</a></h1>
<ul>
<li>This workshop material is heavily inspired by : <ol>
<li>Buffalo, V (2015). <strong><em>Bioinformatics Data Skills</em></strong>.O'Reilly Media, Inc</li>
<li>The Carpentries. <strong><em>The Unix Shell</em></strong> . <a href="https://swcarpentry.github.io/shell-novice/">https://swcarpentry.github.io/shell-novice/</a></li>
<li>The Carpentries. <strong><em>Introduction to Command Line for Genomics</em></strong>. <a href="https://datacarpentry.org/shell-genomics/">https://datacarpentry.org/shell-genomics/</a></li>
<li>Rosalind Project. <a href="https://rosalind.info/about/">https://rosalind.info/about/</a></li>
</ol>
</li>
</ul>
<hr />
<h1 id="license">License<a class="headerlink" href="#license" title="Permanent link">¶</a></h1>
<p>Genomics Aotearoa / New Zealand eScience Infrastructure "Intermediate-Advanced Shell for Bioinformatics" is licensed under the <strong>GNU General Public License v3.0, 29 June 2007</strong> . (<a href="https://github.com/GenomicsAotearoa/shell-for-bioinformatics/blob/main/LICENSE">Follow this link for more information</a>)</p>
<hr />
<h1 id="setup">Setup<a class="headerlink" href="#setup" title="Permanent link">¶</a></h1>
<p>If possible, we do recommend using the <strong>Remote</strong> option over <strong>Local</strong> ( Especially for <em>Windows</em> hosts). This will eliminate the need to install any additional applications</p>
<ul>
<li><strong>Remote</strong> option will require an exiting NeSI Account</li>
</ul>
<h3 id="remote">Remote<a class="headerlink" href="#remote" title="Permanent link">¶</a></h3>
<details class="info">
<summary>Log into NeSI Mahuika Jupyter Service</summary>
<ol>
<li>Follow <a href="https://jupyter.nesi.org.nz/hub/login">https://jupyter.nesi.org.nz/hub/login</a></li>
<li><p>Enter NeSI username, HPC password and 6 digit second factor token<br><img alt="image" src="images/jupyter_login_labels_updated.png" /></p></li>
<li><p>Choose server options as below
<br>>>make sure to choose the correct project code <code>nesi02659</code>, number of CPUs <code>CPUs=4</code>, memory <code>8 GB</code> prior to pressing <img alt="images" src="images/start_button.png" width="40" /> button.</li>
</ol>
<p><br><img alt="images" src="images/jupyter_server2022.png" /></p>
</details>
<h3 id="local">Local <img alt="⚠" class="twemoji" src="https://twemoji.maxcdn.com/v/latest/svg/26a0.svg" title=":warning:" /><a class="headerlink" href="#local" title="Permanent link">¶</a></h3>
<details class="info">
<summary>Local host setup - Windows, MacOS & Linux</summary>
<div class="tabbed-set tabbed-alternate" data-tabs="1:3"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><input id="__tabbed_1_3" name="__tabbed_1" type="radio" /><div class="tabbed-labels"><label for="__tabbed_1_1">Windows Hosts</label><label for="__tabbed_1_2">MacOS</label><label for="__tabbed_1_3">Linux</label></div>
<div class="tabbed-content">
<div class="tabbed-block">
<ul>
<li>Install either </li>
<li>Git for Windows from <a href="https://git-scm.com/download/win">https://git-scm.com/download/win</a> <strong>OR</strong></li>
<li>MobaXterm Home (<em>Portable</em> or <em>Installer</em> edition) from <a href="https://mobaxterm.mobatek.net/download-home-edition.html">https://mobaxterm.mobatek.net/download-home-edition.html</a><ul>
<li>Portable edition does not require administrative privileges </li>
</ul>
</li>
</ul>
</div>
<div class="tabbed-block">
<ul>
<li>Native terminal client is sufficient.</li>
<li>It might not comes with <code>wget</code> download data via command line (can be installed with <code>$ brew install wget</code>)</li>
<li>However, it is not required as we provide a direct link to download data in .zip format </li>
</ul>
</div>
<div class="tabbed-block">
<ul>
<li>Native terminal client is sufficient.</li>
</ul>
</div>
</div>
</div>
<div class="admonition warning">
<p class="admonition-title"><code>bioawk</code> install on all hosts</p>
<p>One of the tools used in this workshop is <code>bioawk</code> which is not native to any terminal clients. Installing it on MacOS and Linux can be done with <code>$ brew install bioawk</code> & <code>$ sudo apt install bioawk</code>, respectively.Windows hosts might have to do it via <code>conda</code> according to <a href="https://anaconda.org/bioconda/bioawk">these instructions</a>. However, this will require a prior install of <strong>Anaconda</strong> Or <strong>Miniconda</strong> </p>
</div>
</details>
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