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34 changes: 20 additions & 14 deletions Download_Installation.qmd
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Expand Up @@ -28,9 +28,9 @@ Please choose your operating system to view how to run MaxQuant.

## MaxQuant on Windows {#sec-mq-windows}

Supported operation system versions (64 bit is required) are Windows 10 or 11 or Windows Server 2016, 2019, 2022.
Supported operation system versions (64-bit is required) are Windows 10 or 11 or Windows Server 2016, 2019, 2022.

- **Install .NET Core 8.0 or higher**: To find out whether you already have it, you can either open the following path. We reccomend using version 8.0.302 at least, as it solves some bugs with the GUI.
- **Install .NET Core 8.0 or higher**: To find out whether you already have it, you can either open the following path. We recommend using version 8.0.302 at least, as it solves some bugs with the GUI.

```{bash}
C:\Program Files\dotnet\sdk
Expand All @@ -44,7 +44,7 @@ dotnet --version

If you need to, you can download the software and get installation instructions e.g. [for .NET 8.0 here](https://dotnet.microsoft.com/en-us/download/dotnet/8.0).

~~.NET 3.1 and older version are not supported anymore.~~
~~.NET 3.1 and older versions are not supported anymore.~~

MaxQuant now works with .NET \>= 8.0.302

Expand All @@ -57,7 +57,7 @@ MaxQuant now works with .NET \>= 8.0.302
We are supporting MaxQuant on Ubuntu 20.04 or higher, but MaxQuant should also work on other distributions of Linux.
~~You may run MaxQuant using Graphical User Interface~~. MaxQuant on Linux doesn't support the use of a GUI at the moment. We're planning to make it available in future versions, [so stay tuned to our newletter](https://maxquant.org/newsletter/), where we'll inform our users about new updates.

This tutorial is focused on running MaxQuant using command line.
This tutorial is focused on running MaxQuant using the command-line.

- **Install .NET Core 8.0** To find out whether you already have it, type in the command line

Expand All @@ -69,7 +69,7 @@ If you see at least version $8.0.302$, then everything is ready to start MaxQuan

Otherwise you need to follow the installation instructions at [.NET Core SDK 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0) for your operating system.

### Global installtion on Ubuntu using `sudo` permissions
### Global installation on Ubuntu using `sudo` permissions

Ubuntu 22.04 (for example)

Expand All @@ -82,7 +82,7 @@ sudo apt-get update && \
sudo apt-get install -y dotnet-sdk-8.0
```

### local installtion using the `conda` environment
### local installation using the `conda` environment

An alternative installation method, which might work better, if no `sudo` rights are available for the user would be to use the `conda` [@anaconda] environment.

Expand All @@ -106,7 +106,7 @@ rm -rf ~/miniconda3/miniconda.sh
```

Before one can use the `conda` environment in your shell, it must be initialized and the session restarted.
Another tip would be to install the mamba package, but **this is only opitional** and is not needed, if you're using conda on a regular basis.
Another tip would be to install the mamba package, but **this is only optional** and is not needed, if you're using conda on a regular basis.
(If you do, you probably already installed mamba 😀).

``` bash
Expand All @@ -120,7 +120,7 @@ mamba init
```

Now, using the `mamba`command one can create a new environment for `dotnet`.
One can either choose a specific version for `dotnet` or by omiting the version number, the atest available version on the anaconda repository will be installed.
One can either choose a specific version for `dotnet` or by omitting the version number, the latest available version on the anaconda repository will be installed.
You can search [here](https://anaconda.org/search?q=dotnet) for possible versions.

Before you can use the tool, you must activate the environment.
Expand All @@ -135,9 +135,9 @@ mamba activate dotnet8
dotnet --version
```

### Scripted installation using Microsoft ressources.
### Scripted installation using Microsoft resources.

One can also follows Microsofts' instruction to install the (optional) latest version of`.NET` by following the script [here](https://dotnet.microsoft.com/en-us/download/dotnet/8.0).
One can also follows Microsoft's instruction to install the (optional) latest version of`.NET` by following the script [here](https://dotnet.microsoft.com/en-us/download/dotnet/8.0).

A manual install has more options to choose from using the `dotnet-install` script from the [.NET page](https://learn.microsoft.com/en-us/dotnet/core/tools/dotnet-install-script).

Expand All @@ -147,17 +147,17 @@ chmod +x ./dotnet-install.sh
./dotnet-install.sh --channel 8.0
```

possible important options here are:
Possible important options here are:

- `--channel` - use this to ask for a specific version and/or subversion
- `--version` - install a specific version
- `--install-dir` - use this to specify the path to the installation directory.

We also added a script for an automated installation of the .NET which can be also downloaded [here](Install_dotnet.sh).
We also added a script for an automated installation of the .NET which can also be downloaded [here](Install_dotnet.sh).
Running the script will ask the user for a download location, where, for now, .NET version 8.0.302 will be installed.
This version was needed due to a bug in Perseus.

After downloading the script it needs to be made executable and can be ran as such:
After downloading the script it needs to be made executable and can be run as such:

```{bash}
chmod -x Install_dotnet.sh
Expand All @@ -174,11 +174,17 @@ You can also use a programmatic way to change that.

If you use on-the fly prediction use this command:

If you use on-the-fly prediction use this command:

``` bash
dotnet MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml --changeFolder new_mqpar.xml <new folder with fasta files> <new folder with raw files>
```

<<<<<<< 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:
>>>>>>> Stashed changes
``` bash
dotnet MaxQuant/bin/MaxQuantCmd.dll old_mqpar.xml --changeFolder new_mqpar.xml <new folder with fasta files> <new folder with raw files> <new folder with libraries>
Expand Down Expand Up @@ -246,4 +252,4 @@ These are mere examples and there is no reason to prefer specific vendors or bra

------------------------------------------------------------------------

For question or problems with the installation we would love to hear from you under [Contact](contact.html).
For questions or problems with the installation we would love to hear from you under [Contact](contact.html).
35 changes: 35 additions & 0 deletions docs/Download_Installation.html
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Expand Up @@ -7,7 +7,11 @@
<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

<title>Download &amp; Installation</title>
<style>
Expand Down Expand Up @@ -233,8 +237,13 @@ <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>
Expand Down Expand Up @@ -271,7 +280,11 @@ <h1 class="title">Download &amp; Installation</h1>
<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
</div>
</div>

Expand Down Expand Up @@ -301,8 +314,13 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="sec-mq-windows"><span cla
<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>
Expand All @@ -313,7 +331,11 @@ <h2 data-number="2.1" class="anchored" data-anchor-id="sec-mq-windows"><span cla
<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 @@ -331,7 +353,11 @@ <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>
Expand Down Expand Up @@ -365,8 +391,13 @@ <h3 data-number="2.2.2" class="anchored" data-anchor-id="local-installation-usin
<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>
Expand All @@ -388,7 +419,11 @@ <h3 data-number="2.2.3" class="anchored" data-anchor-id="scripted-installation-u
</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>
<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>
Expand Down
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