Answers.Body: <p>I have been running MaxQuant quite frequently on Linux. I would use conda to create a dedicated environment and install <code>mono</code>.</p>
  <pre><code># create the environment
  conda create -n maxquant -c conda-forge mono
  # activate the environment
  conda activate maxquant
  # run any maxquant version
  mono /path/to/maxuant/MaxQuantCmd.exe mqpar.xml
  </code></pre>
  <p>This installs a conda environment with <code>mono</code> which is a <code>.NET</code> framework for Linux. I had problems in the past running certain MaxQuant versions that way.</p>
  <p>The <code>mqpar.xml</code> that is required can be created with the MaxQuant GUI. And then the path for input files needs to be contained correctly. The path to the <em>fasta</em> file and the <em>raw</em> file. I would create a template file and then parse these filenames into the specific locations.</p>
  <pre><code># mqpar.xml
  ...
  &lt;fastaFiles&gt;
    &lt;FastaFileInfo&gt;
       &lt;fastaFilePath&gt;__FASTA__&lt;/fastaFilePath&gt;
       &lt;identifierParseRule&gt;&gt;([^\s]*)&lt;/identifierParseRule&gt;
       &lt;descriptionParseRule&gt;&gt;(.*)&lt;/descriptionParseRule&gt;
       &lt;taxonomyParseRule&gt;&lt;/taxonomyParseRule&gt;
       &lt;variationParseRule&gt;&lt;/variationParseRule&gt;
       &lt;modificationParseRule&gt;&lt;/modificationParseRule&gt;
       &lt;taxonomyId&gt;&lt;/taxonomyId&gt;
    &lt;/FastaFileInfo&gt;
  &lt;/fastaFiles&gt;
  ...
  &lt;filePaths&gt;
    &lt;string&gt;__RAW__&lt;/string&gt;
  &lt;/filePaths&gt;
  ...
  </code></pre>
  <p>The combination of <code>maxquant=1.6.10.43</code> and <code>mono=5.14</code> worked and a few other versions. Some versions between 1.6 and 2.x did not work at all.</p>
  <p>Specific versions of MaxQuant are also available directly via <code>conda</code> and there is no need to download the zip file. Instead, you can simply install it with:</p>
  <pre><code>conda install -c conda-forge -c bioconda maxquant mono=5.14
  </code></pre>
  <p>Recently MaxQuant 2 has been added, and not all previous versions are available and run maxquant with:</p>
  <pre><code>maxquant mqpar.xml
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-16T03:40:39.120Z
Answers.LastActivityDate: 2021-09-02T22:18:19.690Z
Answers.LastEditDate: 2021-09-02T22:18:19.690Z
Answers.UserDisplayName: Soerendip
Answers.Body: <p>There is a <a href="https://anaconda.org/bioconda/maxquant" rel="nofollow noreferrer">conda package</a> for maxquant that should work on most platforms (I've used it on CentOS and I think it's been used on Ubuntu as well). There's also a docker container version of that that we (Bioconda) have posted to <a href="https://quay.io/repository/biocontainers/maxquant?tab=tags" rel="nofollow noreferrer">the biocontainers project</a> that should also work.</p>
  
  <p>Please note that large parts of a maxquant analysis are single threaded, regardless of what you specify. We've also had single analysis runs lasting over a month (even when using 90 threads), so the program can be very slow if your search space is large.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-06T17:16:38.493Z
Answers.LastActivityDate: 2020-03-06T17:16:38.493Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I'm trying to run MaxQuant on a linux laptop, hower I'm constantly running into problems with MaxQuant crashing at different stages</p>
  
  <p>I tried to use</p>
  
  <ul>
  <li>mono 6.8</li>
  <li>mono 5.4.1</li>
  </ul>
  
  <p>on </p>
  
  <ul>
  <li>centos</li>
  <li>ubuntu</li>
  </ul>
  
  <p>each with MaxQuant</p>
  
  <ul>
  <li>1.6.3</li>
  <li>1.6.7</li>
  <li>1.6.11</li>
  </ul>
  
  <p>(everything using docker), but I had no success so far.</p>
  
  <p>I also tried to use the ahead of time compilation of mono, also without sucess.
  MQ mostly stalls at the "preparing searches" stage.</p>
  
  <p>Has anyone managed to get MQ running properly on linux and can tell me, which linux distro/version, mono version and MQ version you are using?</p>
  
  <p>Any other help is of course also welcome</p>
  
Tags: <linux><proteomics><mass-spectrometry><maxquant>
Title: Running MaxQuant on Linux
ThreadText: # Running MaxQuant on Linux
  
  (Asked by: username_0 on 2020-03-05)
  
  I'm trying to run MaxQuant on a linux laptop, hower I'm constantly running into problems with MaxQuant crashing at different stages
  
  I tried to use
  
  * mono 6.8
  * mono 5.4.1
  
  on
  
  * centos
  * ubuntu
  
  each with MaxQuant
  
  * 1.6.3
  * 1.6.7
  * 1.6.11
  
  (everything using docker), but I had no success so far.
  
  I also tried to use the ahead of time compilation of mono, also without sucess.
  MQ mostly stalls at the "preparing searches" stage.
  
  Has anyone managed to get MQ running properly on linux and can tell me, which linux distro/version, mono version and MQ version you are using?
  
  Any other help is of course also welcome
  
  **Tags:** linux, proteomics, mass-spectrometry, maxquant
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-03-06. Score: 4 | Accepted answer
  
  There is a [conda package](https://anaconda.org/bioconda/maxquant) for maxquant that should work on most platforms (I've used it on CentOS and I think it's been used on Ubuntu as well). There's also a docker container version of that that we (Bioconda) have posted to [the biocontainers project](https://quay.io/repository/biocontainers/maxquant?tab=tags) that should also work.
  
  Please note that large parts of a maxquant analysis are single threaded, regardless of what you specify. We've also had single analysis runs lasting over a month (even when using 90 threads), so the program can be very slow if your search space is large.
  
  
  ---
  
  ### Answer by username_1 on 2020-07-16. Score: 2
  
  I have been running MaxQuant quite frequently on Linux. I would use conda to create a dedicated environment and install `mono`.
  
  ```
  # create the environment
  conda create -n maxquant -c conda-forge mono
  # activate the environment
  conda activate maxquant
  # run any maxquant version
  mono /path/to/maxuant/MaxQuantCmd.exe mqpar.xml
  
  ```
  
  This installs a conda environment with `mono` which is a `.NET` framework for Linux. I had problems in the past running certain MaxQuant versions that way.
  
  The `mqpar.xml` that is required can be created with the MaxQuant GUI. And then the path for input files needs to be contained correctly. The path to the *fasta* file and the *raw* file. I would create a template file and then parse these filenames into the specific locations.
  
  ```
  # mqpar.xml
  ...
  <fastaFiles>
    <FastaFileInfo>
       <fastaFilePath>__FASTA__</fastaFilePath>
       <identifierParseRule>>([^\s]*)</identifierParseRule>
       <descriptionParseRule>>(.*)</descriptionParseRule>
       <taxonomyParseRule></taxonomyParseRule>
       <variationParseRule></variationParseRule>
       <modificationParseRule></modificationParseRule>
       <taxonomyId></taxonomyId>
    </FastaFileInfo>
  </fastaFiles>
  ...
  <filePaths>
    <string>__RAW__</string>
  </filePaths>
  ...
  
  ```
  
  The combination of `maxquant=1.6.10.43` and `mono=5.14` worked and a few other versions. Some versions between 1.6 and 2.x did not work at all.
  
  Specific versions of MaxQuant are also available directly via `conda` and there is no need to download the zip file. Instead, you can simply install it with:
  
  ```
  conda install -c conda-forge -c bioconda maxquant mono=5.14
  
  ```
  
  Recently MaxQuant 2 has been added, and not all previous versions are available and run maxquant with:
  
  ```
  maxquant mqpar.xml
  
  ```
  
  
  ---
  
  