correcting typos

Download_Installation.qmd

@@ -127,7 +127,7 @@ mamba activate dotnet7
 dotnet --version
 ```
 
-### Scripted installtion using Microsoft ressources.
+### Scripted installation using Microsoft ressources.
 
 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).
 

docs/Download_Installation.html

@@ -235,7 +235,7 @@ <h2 id="toc-title">On this page</h2>
   <ul class="collapse">
   <li><a href="#global-installtion-on-ubuntu-using-sudo-permissions" id="toc-global-installtion-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 installtion on Ubuntu using <code>sudo</code> permissions</a></li>
   <li><a href="#local-installtion-using-the-conda-environment" id="toc-local-installtion-using-the-conda-environment" class="nav-link" data-scroll-target="#local-installtion-using-the-conda-environment"><span class="header-section-number">2.2.2</span> local installtion using the <code>conda</code> environment</a></li>
-  <li><a href="#scripted-installtion-using-microsoft-ressources." id="toc-scripted-installtion-using-microsoft-ressources." class="nav-link" data-scroll-target="#scripted-installtion-using-microsoft-ressources."><span class="header-section-number">2.2.3</span> Scripted installtion using Microsoft ressources.</a></li>
+  <li><a href="#scripted-installation-using-microsoft-ressources." id="toc-scripted-installation-using-microsoft-ressources." class="nav-link" data-scroll-target="#scripted-installation-using-microsoft-ressources."><span class="header-section-number">2.2.3</span> Scripted installation using Microsoft ressources.</a></li>
   </ul></li>
   </ul></li>
   <li><a href="#hardware-requirements" id="toc-hardware-requirements" class="nav-link" data-scroll-target="#hardware-requirements"><span class="header-section-number">3</span> Hardware requirements</a>
@@ -359,8 +359,8 @@ <h3 data-number="2.2.2" class="anchored" data-anchor-id="local-installtion-using
 <span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="co">#To test that we do have `dotnet`</span></span>
 <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-installtion-using-microsoft-ressources." class="level3" data-number="2.2.3">
-<h3 data-number="2.2.3" class="anchored" data-anchor-id="scripted-installtion-using-microsoft-ressources."><span class="header-section-number">2.2.3</span> Scripted installtion using Microsoft ressources.</h3>
+<section id="scripted-installation-using-microsoft-ressources." class="level3" data-number="2.2.3">
+<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 ressources.</h3>
 <p>One can also follows Microsofts’ 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>
 <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>

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 nother distributions 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.\n\n2.2.1 Global installtion on Ubuntu using sudo permissions\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\n\n2.2.2 local installtion using the conda environment\nAn alternative installation method, which might work better, if no sudo rights are available for the user would be to use the conda (“Anaconda Software Distribution” 2020) environment.\nDepending on your architecture, the user must choose between the x86 and the Arm installation scripts. Both can be downloaded from the anaconda repository using the wget command.\n# Or use conda to install an environment\n## get the installer \nmkdir -p ~/miniconda3\n# for 64x-bit 86x architecture\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh\n# for 64-bit arm architecture\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O ~/miniconda3/miniconda.sh\n\n### You'll only need one the above two scripts!!!\n\n# Install the conda base env\nbash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3\nrm -rf ~/miniconda3/miniconda.sh\nBefore 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. (If you do, you probably already installed mamba 😀).\n# initialize conda on bash \n~/miniconda3/bin/conda init bash\n~/miniconda3/bin/conda init zsh\n# logging out and back in again\nconda install conda-forge::mamba\nmamba init \n#Here again, one must log out and back in again for mamba to be active. \nNow, using the mambacommand 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. You can search here for possible versions.\nBefore you can use the tool, you must activate the environment. Last check to see if the installation was successful, one can check for the available dotnet version.\n#Now we create `dotnet` env\n# create the dotnet env\nmamba create -n dotnet7 conda-forge::dotnet=7.0.404 \nmamba activate dotnet7\n#To test that we do have `dotnet`\ndotnet --version\n\n\n2.2.3 Scripted installtion using Microsoft ressources.\nOne can also follows Microsofts’ instruction to install the (optional) latest version of.NET by following the script here.\nA manual install has more options to choose from using the dotnet-install script from the .NET page.\nwget https://dot.net/v1/dotnet-install.sh -O dotnet-install.sh\nchmod +x ./dotnet-install.sh\n./dotnet-install.sh --channel 7.0\npossible important options here are:\n\n--channel - use this to ask for a specific version and/or subversion\n--version - install a specific version\n--install-dir - use this to specify the path to the installation directory.\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"
+    "text": "2.2 MaxQuant on Linux\nWe are supporting MaxQuant on Ubuntu 20.04 or higher, but MaxQuant should also work on nother distributions 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.\n\n2.2.1 Global installtion on Ubuntu using sudo permissions\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\n\n2.2.2 local installtion using the conda environment\nAn alternative installation method, which might work better, if no sudo rights are available for the user would be to use the conda (“Anaconda Software Distribution” 2020) environment.\nDepending on your architecture, the user must choose between the x86 and the Arm installation scripts. Both can be downloaded from the anaconda repository using the wget command.\n# Or use conda to install an environment\n## get the installer \nmkdir -p ~/miniconda3\n# for 64x-bit 86x architecture\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh\n# for 64-bit arm architecture\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh -O ~/miniconda3/miniconda.sh\n\n### You'll only need one the above two scripts!!!\n\n# Install the conda base env\nbash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3\nrm -rf ~/miniconda3/miniconda.sh\nBefore 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. (If you do, you probably already installed mamba 😀).\n# initialize conda on bash \n~/miniconda3/bin/conda init bash\n~/miniconda3/bin/conda init zsh\n# logging out and back in again\nconda install conda-forge::mamba\nmamba init \n#Here again, one must log out and back in again for mamba to be active. \nNow, using the mambacommand 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. You can search here for possible versions.\nBefore you can use the tool, you must activate the environment. Last check to see if the installation was successful, one can check for the available dotnet version.\n#Now we create `dotnet` env\n# create the dotnet env\nmamba create -n dotnet7 conda-forge::dotnet=7.0.404 \nmamba activate dotnet7\n#To test that we do have `dotnet`\ndotnet --version\n\n\n2.2.3 Scripted installation using Microsoft ressources.\nOne can also follows Microsofts’ instruction to install the (optional) latest version of.NET by following the script here.\nA manual install has more options to choose from using the dotnet-install script from the .NET page.\nwget https://dot.net/v1/dotnet-install.sh -O dotnet-install.sh\nchmod +x ./dotnet-install.sh\n./dotnet-install.sh --channel 7.0\npossible important options here are:\n\n--channel - use this to ask for a specific version and/or subversion\n--version - install a specific version\n--install-dir - use this to specify the path to the installation directory.\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",