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yeroslaviz committed Nov 28, 2024
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93 changes: 35 additions & 58 deletions docs/Download_Installation.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.555">
<meta name="generator" content="quarto-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

<meta name="author" content="Cox Lab">
<<<<<<< Updated upstream
<meta name="dcterms.date" content="2024-07-23">
=======
<meta name="dcterms.date" content="2024-08-14">
>>>>>>> Stashed changes
<meta name="dcterms.date" content="2024-11-28">

<title>Download &amp; Installation</title>
<style>
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<script type="text/javascript">
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</a>
</div>
<div id="quarto-search" class="" title="Search"></div>
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<div class="collapse navbar-collapse" id="navbarCollapse">
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</li>
</ul>
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<div class="quarto-navbar-tools">
<div class="quarto-navbar-tools">
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Expand All @@ -237,13 +233,8 @@ <h2 id="toc-title">On this page</h2>
<li><a href="#sec-mq-windows" id="toc-sec-mq-windows" class="nav-link" data-scroll-target="#sec-mq-windows"><span class="header-section-number">2.1</span> MaxQuant on Windows</a></li>
<li><a href="#maxquant-on-linux" id="toc-maxquant-on-linux" class="nav-link" data-scroll-target="#maxquant-on-linux"><span class="header-section-number">2.2</span> MaxQuant on Linux</a>
<ul class="collapse">
<<<<<<< Updated upstream
<li><a href="#global-installation-on-ubuntu-using-sudo-permissions" id="toc-global-installation-on-ubuntu-using-sudo-permissions" class="nav-link" data-scroll-target="#global-installtion-on-ubuntu-using-sudo-permissions"><span class="header-section-number">2.2.1</span> Global installation on Ubuntu using <code>sudo</code> permissions</a></li>
<li><a href="#local-installation-using-the-conda-environment" id="toc-local-installation-using-the-conda-environment" class="nav-link" data-scroll-target="#local-installation-using-the-conda-environment"><span class="header-section-number">2.2.2</span> Local installation using the <code>conda</code> environment</a></li>
=======
<li><a href="#global-installation-on-ubuntu-using-sudo-permissions" id="toc-global-installation-on-ubuntu-using-sudo-permissions" class="nav-link" data-scroll-target="#global-installation-on-ubuntu-using-sudo-permissions"><span class="header-section-number">2.2.1</span> Global installation on Ubuntu using <code>sudo</code> permissions</a></li>
<li><a href="#local-installation-using-the-conda-environment" id="toc-local-installation-using-the-conda-environment" class="nav-link" data-scroll-target="#local-installation-using-the-conda-environment"><span class="header-section-number">2.2.2</span> local installation using the <code>conda</code> environment</a></li>
>>>>>>> Stashed changes
<li><a href="#scripted-installation-using-microsoft-resources." id="toc-scripted-installation-using-microsoft-resources." class="nav-link" data-scroll-target="#scripted-installation-using-microsoft-resources."><span class="header-section-number">2.2.3</span> Scripted installation using Microsoft resources.</a></li>
</ul></li>
<li><a href="#edit-mqpar.xml-file" id="toc-edit-mqpar.xml-file" class="nav-link" data-scroll-target="#edit-mqpar.xml-file"><span class="header-section-number">2.3</span> Edit mqpar.xml file</a></li>
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<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<<<<<<< Updated upstream
<p class="date">July 23, 2024</p>
=======
<p class="date">August 14, 2024</p>
>>>>>>> Stashed changes
<p class="date">November 28, 2024</p>
</div>
</div>

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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">C:\Program</span> Files<span class="dt">\d</span>otnet<span class="dt">\s</span>dk</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>or run the following command in the terminal (Win+R -&gt; <code>cmd</code>):</p>
<<<<<<< Updated upstream
<div class="sourceCode" 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">dotnet</span> <span class="at">--version</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>If you need to, you can download the software and get installation instructions e.g.&nbsp;<a href="https://dotnet.microsoft.com/en-us/download/dotnet/8.0">for .NET 8.0 here</a>.</p>
=======
<div class="sourceCode" 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">dotnat</span> <span class="at">--version</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>If you need to, you can download the software and get installation instructions at the <a href="https://dotnet.microsoft.com/en-us/download/dotnet/8.0">for .NET 8.0 here</a>.</p>
>>>>>>> Stashed changes
<p><del>.NET 3.1 and older versions are not supported anymore.</del></p>
<p>MaxQuant now works with .NET &gt;= 8.0.302</p>
<ul>
<li><p><strong>Run MaxQuant GUI</strong> Double click on <code>MaxQuant.exe</code> in the <code>MaxQuant</code> folder and specify your RAW files, experimental design, and fasta files.</p></li>
<li><p><strong>Run MaxQuant GUI</strong> Double click on <code>MaxQuant.exe</code> in the <code>MaxQuant</code> folder and specify your RAW files, experimental design and fasta files.</p></li>
<li><p><strong>Start MaxQuant</strong> Click on the <code>Start</code> button.</p></li>
</ul>
</section>
<section id="maxquant-on-linux" class="level2" data-number="2.2">
<h2 data-number="2.2" class="anchored" data-anchor-id="maxquant-on-linux"><span class="header-section-number">2.2</span> MaxQuant on Linux</h2>
<p>We are supporting MaxQuant on Ubuntu 20.04 or higher, but MaxQuant should also work on other distributions of Linux. <del>You may run MaxQuant using Graphical User Interface</del>. MaxQuant on Linux doesn’t support the use of a GUI at the moment. We’re planning to make it available in future versions, <a href="https://maxquant.org/newsletter/">so stay tuned to our newletter</a>, where we’ll inform our users about new updates.</p>
<<<<<<< Updated upstream
<p>This tutorial is focused on running MaxQuant using the command-line interface.</p>
=======
<p>This tutorial is focused on running MaxQuant using the command-line.</p>
>>>>>>> Stashed changes
<ul>
<li><strong>Install .NET Core 8.0</strong> To find out whether you already have it, type in the command line</li>
</ul>
Expand All @@ -353,11 +331,7 @@ <h3 data-number="2.2.1" class="anchored" data-anchor-id="global-installation-on-
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt-get install <span class="at">-y</span> dotnet-sdk-8.0</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="local-installation-using-the-conda-environment" class="level3" data-number="2.2.2">
<<<<<<< Updated upstream
<h3 data-number="2.2.2" class="anchored" data-anchor-id="local-installation-using-the-conda-environment"><span class="header-section-number">2.2.2</span> Local installation using the <code>conda</code> environment</h3>
=======
<h3 data-number="2.2.2" class="anchored" data-anchor-id="local-installation-using-the-conda-environment"><span class="header-section-number">2.2.2</span> local installation using the <code>conda</code> environment</h3>
>>>>>>> Stashed changes
<p>An alternative installation method, which might work better, if no <code>sudo</code> rights are available for the user would be to use the <code>conda</code> <span class="citation" data-cites="anaconda">(<a href="#ref-anaconda" role="doc-biblioref"><span>“Anaconda Software Distribution”</span> 2020</a>)</span> environment.</p>
<p>Depending on your architecture, the user must choose between the x86 and the Arm installation scripts. Both can be downloaded from the <a href="https://repo.anaconda.com/miniconda/">anaconda repository</a> using the <code>wget</code> command.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Or use conda to install an environment</span></span>
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<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> <span class="at">--version</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="scripted-installation-using-microsoft-resources." class="level3" data-number="2.2.3">
<<<<<<< Updated upstream
<h3 data-number="2.2.3" class="anchored" data-anchor-id="scripted-installation-using-microsoft-ressources."><span class="header-section-number">2.2.3</span> Scripted installation using Microsoft resources.</h3>
<p>One can also follow Microsoft’s instruction to install the (optional) latest version of<code>.NET</code> by following the script <a href="https://dotnet.microsoft.com/en-us/download/dotnet/8.0">here</a>.</p>
=======
<h3 data-number="2.2.3" class="anchored" data-anchor-id="scripted-installation-using-microsoft-resources."><span class="header-section-number">2.2.3</span> Scripted installation using Microsoft resources.</h3>
<p>One can also follows Microsoft’s instruction to install the (optional) latest version of<code>.NET</code> by following the script <a href="https://dotnet.microsoft.com/en-us/download/dotnet/8.0">here</a>.</p>
>>>>>>> Stashed changes
<p>A manual install has more options to choose from using the <code>dotnet-install</code> script from the <a href="https://learn.microsoft.com/en-us/dotnet/core/tools/dotnet-install-script">.NET page</a>.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span> https://dot.net/v1/dotnet-install.sh <span class="at">-O</span> dotnet-install.sh</span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">chmod</span> +x ./dotnet-install.sh</span>
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</section>
<section id="edit-mqpar.xml-file" class="level2" data-number="2.3">
<h2 data-number="2.3" class="anchored" data-anchor-id="edit-mqpar.xml-file"><span class="header-section-number">2.3</span> Edit mqpar.xml file</h2>
<<<<<<< Updated upstream
<p>Currently we highly recommend to pre-configure the <code>mqpar.xml</code> file in MaxQuant GUI. After transferring the file on Linux machine, do not forget to update file addresses accordingly. You can also use a programmatic way to change that.</p>
=======
<p>Currently we highly recommend to preconfigure the <code>mqpar.xml</code> file in MaxQuant GUI. After transferring the file on Linux machine, do not forget to update file addresses accordingly. You can also use a programmatic way to change that.</p>
>>>>>>> Stashed changes
<p>If you use on-the fly prediction use this command:</p>
<p>If you use on-the-fly prediction use this command:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml <span class="at">--changeFolder</span> new_mqpar.xml <span class="op">&lt;</span>new folder with fasta files<span class="op">&gt;</span> <span class="op">&lt;</span>new folder with raw files<span class="op">&gt;</span> </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>If you use predicted libraries, you also need to add the path to the saved libraries, so use this command:</p>
<p>&lt;&lt;&lt;&lt;&lt;&lt;&lt; Updated upstream If you use predicted libraries, you need to also add the path to the saved libraries, so use this command: ======= If you use predicted libraries, you also need to add the path to the saved libraries, so use this command: &gt;&gt;&gt;&gt;&gt;&gt;&gt; Stashed changes</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml <span class="at">--changeFolder</span> new_mqpar.xml <span class="op">&lt;</span>new folder with fasta files<span class="op">&gt;</span> <span class="op">&lt;</span>new folder with raw files<span class="op">&gt;</span> <span class="op">&lt;</span>new folder with libraries<span class="op">&gt;</span> </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>However if you feel familiar with a structure of <code>mqpar.xml</code>, you may create a template of <code>mqpar.xml</code> and edit it directly.</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.dll <span class="at">--create</span> new_mqpar.xml</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</body></html>
</body></html>
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