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<h1 class="quarto-secondary-nav-title"><span class="chapter-number">1</span> <span class="chapter-title">Installation of the <em>OBITools</em></span></h1>
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<a href="./">OBITools V4</a>
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<a href="./index.html" class="sidebar-item-text sidebar-link">Preface</a>
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<a href="./installation.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">1</span> <span class="chapter-title">Installation of the <em>OBITools</em></span></a>
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<a href="./formats.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">File formats usable with <em>OBITools</em></span></a>
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<a href="./tutorial.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">OBITools V4 Tutorial</span></a>
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<a href="./commands.html" class="sidebar-item-text sidebar-link">The *OBITools V4* commands</a>
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<a href="./inupt.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">Specifying the data input to <em>OBITools</em> commands</span></a>
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<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
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<a href="./common_options.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></a>
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<div class="sidebar-item-container">
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<a href="./expressions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></a>
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</div>
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<a href="./comm_metabarcode_design.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span> <span class="chapter-title">Metabarcode design and quality assessment</span></a>
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</div>
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<li class="sidebar-item">
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<a href="./comm_reformat.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span> <span class="chapter-title">File format conversions</span></a>
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</div>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./comm_annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></a>
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</div>
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<li class="sidebar-item">
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<a href="./comm_computation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></a>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
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</div>
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<li class="sidebar-item">
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<a href="./comm_utilities.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></a>
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</div>
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</ul>
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</li>
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<li class="sidebar-item sidebar-item-section">
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<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
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<a href="./annexes.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">A</span> <span class="chapter-title">Annexes</span></a>
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<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
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<nav id="TOC" role="doc-toc" class="toc-active">
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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#availability-of-the-obitools" id="toc-availability-of-the-obitools" class="nav-link active" data-scroll-target="#availability-of-the-obitools"><span class="toc-section-number">1.1</span> Availability of the <em>OBITools</em></a></li>
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<li><a href="#prerequisites" id="toc-prerequisites" class="nav-link" data-scroll-target="#prerequisites"><span class="toc-section-number">1.2</span> Prerequisites</a></li>
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<li><a href="#installation-with-the-install-script" id="toc-installation-with-the-install-script" class="nav-link" data-scroll-target="#installation-with-the-install-script"><span class="toc-section-number">1.3</span> Installation with the install script</a></li>
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<li><a href="#compilation-from-sources" id="toc-compilation-from-sources" class="nav-link" data-scroll-target="#compilation-from-sources"><span class="toc-section-number">1.4</span> Compilation from sources</a></li>
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<header id="title-block-header" class="quarto-title-block default">
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<div class="quarto-title">
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<h1 class="title d-none d-lg-block"><span class="chapter-number">1</span> <span class="chapter-title">Installation of the <em>OBITools</em></span></h1>
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</div>
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<div class="quarto-title-meta">
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</header>
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<section id="availability-of-the-obitools" class="level2" data-number="1.1">
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<h2 data-number="1.1" class="anchored" data-anchor-id="availability-of-the-obitools"><span class="header-section-number">1.1</span> Availability of the <em>OBITools</em></h2>
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<p>The <em>OBITools</em> are open source and protected by the <a href="http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html">CeCILL 2.1 license</a>.</p>
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<p>All the sources of the <a href="http://metabarcoding.org/obitools4"><em>OBITools4</em></a> can be downloaded from the metabarcoding git server (https://git.metabarcoding.org).</p>
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</section>
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<section id="prerequisites" class="level2" data-number="1.2">
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<h2 data-number="1.2" class="anchored" data-anchor-id="prerequisites"><span class="header-section-number">1.2</span> Prerequisites</h2>
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<p>The <em>OBITools4</em> are developped using the <a href="https://go.dev/">GO programming language</a>, we stick to the latest version of the language, today the <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mn>1.21</mn><mn>.4</mn></mrow><annotation encoding="application/x-tex">1.21.4</annotation></semantics></math>. If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. Some parts of the soft are also written in C, therefore a recent C compiler is also requested, GCC on Linux or Windows, the Developer Tools on Mac.</p>
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<p>Whatever the installation you decide for, you will have to ensure that a C compiler is available on your system.</p>
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</section>
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<section id="installation-with-the-install-script" class="level2" data-number="1.3">
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<h2 data-number="1.3" class="anchored" data-anchor-id="installation-with-the-install-script"><span class="header-section-number">1.3</span> Installation with the install script</h2>
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<p>An installation script that compiles the new <em>OBITools</em> on your Unix-like system is available online. The easiest way to run it is to copy and paste the following command into your terminal</p>
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<div class="cell" data-execution_count="1">
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<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-L</span> https://metabarcoding.org/obitools4/install.sh <span class="kw">|</span> <span class="fu">bash</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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<p>By default, the script installs the <em>OBITools</em> commands and other associated files into the <code>/usr/local</code> directory. The names of the commands in the new <em>OBITools4</em> are mostly identical to those in <em>OBITools2</em>. Therefore, installing the new <em>OBITools</em> may hide or delete the old ones. If you want both versions to be available on your system, the installation script offers two options:</p>
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<blockquote class="blockquote">
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<p>-i, –install-dir Directory where <em>OBITools</em> are installed (as example use <code>/usr/local</code> not <code>/usr/local/bin</code>).</p>
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<p>-p, –obitools-prefix Prefix added to the <em>OBITools</em> command names if you want to have several versions of obitools at the same time on your system (as example <code>-p g</code> will produce <code>gobigrep</code> command instead of <code>obigrep</code>).</p>
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</blockquote>
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<p>You can use these options by following the installation command:</p>
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<div class="cell" data-execution_count="2">
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<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-L</span> https://metabarcoding.org/obitools4/install.sh <span class="kw">|</span> <span class="dt">\</span></span>
|
||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">bash</span> <span class="at">-s</span> <span class="at">--</span> <span class="at">--install-dir</span> test_install <span class="at">--obitools-prefix</span> k</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
</div>
|
||
<p>In this case, the binaries will be installed in the <code>test_install</code> directory and all command names will be prefixed with the letter <code>k</code>. Thus <code>obigrep</code> will be named <code>kobigrep</code>.</p>
|
||
</section>
|
||
<section id="compilation-from-sources" class="level2" data-number="1.4">
|
||
<h2 data-number="1.4" class="anchored" data-anchor-id="compilation-from-sources"><span class="header-section-number">1.4</span> Compilation from sources</h2>
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|
||
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<nav class="page-navigation">
|
||
<div class="nav-page nav-page-previous">
|
||
<a href="./intro.html" class="pagination-link">
|
||
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">The OBITools</span>
|
||
</a>
|
||
</div>
|
||
<div class="nav-page nav-page-next">
|
||
<a href="./formats.html" class="pagination-link">
|
||
<span class="nav-page-text"><span class="chapter-number">2</span> <span class="chapter-title">File formats usable with <em>OBITools</em></span></span> <i class="bi bi-arrow-right-short"></i>
|
||
</a>
|
||
</div>
|
||
</nav>
|
||
</div> <!-- /content -->
|
||
|
||
|
||
|
||
</body></html> |