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maxquant:common:download_and_installation

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maxquant:common:download_and_installation [2020/11/21 00:15]
sinitcyn [Hardware requirements]
maxquant:common:download_and_installation [2020/11/21 00:41] (current)
sinitcyn [Download]
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 Supported operation system versions (64 bit is required) are Windows Vista, 7, 8, 10, Server 2008, 2012. Supported operation system versions (64 bit is required) are Windows Vista, 7, 8, 10, Server 2008, 2012.
  
-  * **Install .NET Framework 4.7.or higher** \\ To find out whether you already have it, follow the instructions on [[http://​msdn.microsoft.com/​en-us/​library/​hh925568%28v=vs.110%29.aspx#​net_b|How to Determine Which .NET Framework Versions Are Installed]]. If you need to, you can download the software and get installation instructions at the [[http://​www.microsoft.com/​en-us/​download/​details.aspx?​id=30653|Microsoft Download Center]].+  * **Install .NET Framework 4.7.or higher** \\ To find out whether you already have it, follow the instructions on [[http://​msdn.microsoft.com/​en-us/​library/​hh925568%28v=vs.110%29.aspx#​net_b|How to Determine Which .NET Framework Versions Are Installed]]. If you need to, you can download the software and get installation instructions at the [[http://​www.microsoft.com/​en-us/​download/​details.aspx?​id=30653|Microsoft Download Center]]. 
   * **Run MaxQuant GUI**   * **Run MaxQuant GUI**
 Double click on //​MaxQuant.exe//​ in //​MaxQuant//​ folder and specify your RAW files, experimental design and fasta files. Double click on //​MaxQuant.exe//​ in //​MaxQuant//​ folder and specify your RAW files, experimental design and fasta files.
 +
   *  **Start MaxQuant**   *  **Start MaxQuant**
 Click on the //Start// button. Click on the //Start// button.
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 -->​MaxQuant on Linux# -->​MaxQuant on Linux#
-We are supporting ​and testing ​MaxQuant on Ubuntu 16.04.3 or higher, but MaxQuant should also work on another distribution of Linux. \\+We are supporting MaxQuant on Ubuntu 16 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 for //MaxQuant on Windows// starting from second point. This tutorial is focused on running MaxQuant using command line. You may run MaxQuant using Graphical User Interface. In this case, you should install Mono and follow instructions for //MaxQuant on Windows// starting from second point. This tutorial is focused on running MaxQuant using command line.
  
-  ​* **Install ​Mono Framework 5.4.1 or higher** \\ + 
 +  ​* **Install .NET Core 2.1** \\ 
 To find out whether you already have it, type in the command line To find out whether you already have it, type in the command line
 <code bash> <code bash>
-mono --version+dotnet ​--version
 </​code>​ </​code>​
-If you need to, you can download the software and get installation instructions at the [[http://www.mono-project.com/​download/​#download-lin|Mono Download page]].+If you see the version //2.1.811//then everything is ready to start MaxQuant. 
 + 
 +Overwise ​you need to get installation instructions at the [[https://dotnet.microsoft.com/​download/​dotnet-core/2.1|.NET Core SDK 2.1.811]] for your operation system. 
 +--> Ubuntu 20.04 (for example) 
 +<code bash> 
 +wget https://​packages.microsoft.com/​config/​ubuntu/​20.04/​packages-microsoft-prod.deb -O packages-microsoft-prod.deb 
 +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 
 +</​code>​ 
 +<-- 
 + 
   * **Edit //​mqpar.xml//​ file**   * **Edit //​mqpar.xml//​ file**
-Currently 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.+Currently 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. 
 +<code bash> 
 +dotnet MaxQuant/​bin/​MaxQuantCmd.exe --changeFolder=new_mqpar.xml <new folder with fasta files> <new folder with raw files> old_mqpar.xml 
 +</​code>​ 
 +However if you feel familiar with a structure of mqpar.xml, you may create a template of mqpar.xml and edit it directly. 
 +<code bash> 
 +dotnet MaxQuant/​bin/​MaxQuantCmd.exe --create new_mqpar.xml 
 +</​code>​ 
 + 
   * **Run MaxQuant**   * **Run MaxQuant**
 <code bash> <code bash>
-mono MaxQuant/​bin/​MaxQuantCmd.exe mqpar.xml+dotnet ​MaxQuant/​bin/​MaxQuantCmd.exe mqpar.xml
 </​code>​ </​code>​
 <-- <--
maxquant/common/download_and_installation.txt · Last modified: 2020/11/21 00:41 by sinitcyn