update maxquant on linux installation

exe to dll

Download_Installation.qmd

@@ -73,7 +73,7 @@ sudo dpkg -i packages-microsoft-prod.deb
 sudo apt-get update; \
 sudo apt-get install -y apt-transport-https && \
 sudo apt-get update && \
-sudo apt-get install -y dotnet-sdk-2.1
+sudo apt-get install -y dotnet-sdk-7.0
 ```
 
 -   **Edit mqpar.xml file**
@@ -82,19 +82,19 @@ Currently we highly recommend to preconfigure the `mqpar.xml` file in MaxQuant G
 You can also use a programmatic way to change that.
 
 ``` bash
-dotnet MaxQuant/bin/MaxQuantCmd.exe --changeFolder=new_mqpar.xml <new folder with fasta files> <new folder with raw files> old_mqpar.xml
+dotnet MaxQuant/bin/MaxQuantCmd.dll --changeFolder=new_mqpar.xml <new folder with fasta files> <new folder with raw files> old_mqpar.xml
 ```
 
 However if you feel familiar with a structure of `mqpar.xml`, you may create a template of `mqpar.xml` and edit it directly.
 
 ``` bash
-dotnet MaxQuant/bin/MaxQuantCmd.exe --create new_mqpar.xml
+dotnet MaxQuant/bin/MaxQuantCmd.dll --create new_mqpar.xml
 ```
 
 -   **Run MaxQuant**
 
 ``` bash
-dotnet MaxQuant/bin/MaxQuantCmd.exe mqpar.xml
+dotnet MaxQuant/bin/MaxQuantCmd.dll mqpar.xml
 ```
 
 # Hardware requirements

docs/Download_Installation.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Cox Lab">
-<meta name="dcterms.date" content="2024-03-18">
+<meta name="dcterms.date" content="2024-04-10">
 
 <title>Download &amp; Installation</title>
 <style>
@@ -215,7 +215,7 @@ <h1 class="title">Download &amp; Installation</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">March 18, 2024</p>
+      <p class="date">April 10, 2024</p>
     </div>
   </div>
 
@@ -265,18 +265,18 @@ <h2 data-number="2.2" class="anchored" data-anchor-id="maxquant-on-linux"><span
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt-get update<span class="kw">;</span> <span class="dt">\</span></span>
 <span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt-get install <span class="at">-y</span> apt-transport-https <span class="kw">&amp;&amp;</span> <span class="dt">\</span></span>
 <span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt-get update <span class="kw">&amp;&amp;</span> <span class="dt">\</span></span>
-<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-2.1</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<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-7.0</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <ul>
 <li><strong>Edit mqpar.xml file</strong></li>
 </ul>
 <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>
-<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="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.exe <span class="at">--changeFolder</span><span class="op">=</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> old_mqpar.xml</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<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="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.dll <span class="at">--changeFolder</span><span class="op">=</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> old_mqpar.xml</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="cb6"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.exe <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>
+<div class="sourceCode" id="cb6"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" 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>
 <ul>
 <li><strong>Run MaxQuant</strong></li>
 </ul>
-<div class="sourceCode" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.exe mqpar.xml</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dotnet</span> MaxQuant/bin/MaxQuantCmd.dll mqpar.xml</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section>
 </section>
 <section id="hardware-requirements" class="level1" data-number="3">

docs/search.json

@@ -3497,7 +3497,7 @@
     "href": "Download_Installation.html#maxquant-on-linux",
     "title": "Download & Installation",
     "section": "2.2 MaxQuant on Linux",
-    "text": "2.2 MaxQuant on Linux\nWe are supporting MaxQuant on Ubuntu 20.04 or higher, but MaxQuant should also work on another distribution of Linux. You may run MaxQuant using Graphical User Interface. In this case, you should install Mono and follow instructions in Section 2.1 for MaxQuant on Windows starting from second point. This tutorial is focused on running MaxQuant using command line.\n\nInstall .NET Core 7.0 To find out whether you already have it, type in the command line\n\ndotnet --version\nIf you see at least version \\(7.0.407\\), then everything is ready to start MaxQuant.\nOtherwise you need to follow the installation instructions at .NET Core SDK 7.0 for your operating system.\nUbuntu 22.04 (for example)\nwget https://packages.microsoft.com/config/ubuntu/20.04/packages-microsoft-prod.deb -O packages-microsoft-prod.deb\nsudo dpkg -i packages-microsoft-prod.deb\nsudo apt-get update; \\\nsudo apt-get install -y apt-transport-https && \\\nsudo apt-get update && \\\nsudo apt-get install -y dotnet-sdk-2.1\n\nEdit mqpar.xml file\n\nCurrently we highly recommend to preconfigure the mqpar.xml 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.\ndotnet MaxQuant/bin/MaxQuantCmd.exe --changeFolder=new_mqpar.xml <new folder with fasta files> <new folder with raw files> old_mqpar.xml\nHowever if you feel familiar with a structure of mqpar.xml, you may create a template of mqpar.xml and edit it directly.\ndotnet MaxQuant/bin/MaxQuantCmd.exe --create new_mqpar.xml\n\nRun MaxQuant\n\ndotnet MaxQuant/bin/MaxQuantCmd.exe mqpar.xml"
+    "text": "2.2 MaxQuant on Linux\nWe are supporting MaxQuant on Ubuntu 20.04 or higher, but MaxQuant should also work on another distribution of Linux. You may run MaxQuant using Graphical User Interface. In this case, you should install Mono and follow instructions in Section 2.1 for MaxQuant on Windows starting from second point. This tutorial is focused on running MaxQuant using command line.\n\nInstall .NET Core 7.0 To find out whether you already have it, type in the command line\n\ndotnet --version\nIf you see at least version \\(7.0.407\\), then everything is ready to start MaxQuant.\nOtherwise you need to follow the installation instructions at .NET Core SDK 7.0 for your operating system.\nUbuntu 22.04 (for example)\nwget https://packages.microsoft.com/config/ubuntu/20.04/packages-microsoft-prod.deb -O packages-microsoft-prod.deb\nsudo dpkg -i packages-microsoft-prod.deb\nsudo apt-get update; \\\nsudo apt-get install -y apt-transport-https && \\\nsudo apt-get update && \\\nsudo apt-get install -y dotnet-sdk-7.0\n\nEdit mqpar.xml file\n\nCurrently we highly recommend to preconfigure the mqpar.xml 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.\ndotnet MaxQuant/bin/MaxQuantCmd.dll --changeFolder=new_mqpar.xml <new folder with fasta files> <new folder with raw files> old_mqpar.xml\nHowever if you feel familiar with a structure of mqpar.xml, you may create a template of mqpar.xml and edit it directly.\ndotnet MaxQuant/bin/MaxQuantCmd.dll --create new_mqpar.xml\n\nRun MaxQuant\n\ndotnet MaxQuant/bin/MaxQuantCmd.dll mqpar.xml"
   },
   {
     "objectID": "cyclicannotation.html",