Difference between revisions of "Install MicrobeMS"

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* It is recommended to create an additional directory ''mass'' in the existing toolbox directory structure of the Matlab installation. The complete path to the toolbox directory should be similar to ''C:\program files\Matlab\R20XYx\toolbox\matlab\mass'' (''R20XYa'' - denotes the Matlab release version) and ''C:\program files\Matlab\R20XYx'' equals the variable ''matlabroot''. You can check this variable by typing
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* Download and unzip the MicrobeMS archive ''  pcode-microbems-v0XX.zip'' (see [[download_MicrobeMS|Downloading MicrobeMS]])
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* It is recommended to create an additional subdirectory ''mass'' in the directory ''C:\Users\YourUserName\Documents\Matlab'' (Windows) or in the ''/home/YourUserName'' path (LINUX). Copy then all files into the new folder.
 
   
 
   
     >> matlabroot
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* Start Matlab and enter at the command prompt
<ul>
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at the Matlab command prompt. Note that the directory ''C:\program files\Matlab\R20XYx\toolbox\matlab'' should contain additional subdirectories such as ''\winfun'' oder ''\timefun''.
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     >> addpath(''FullPathToMass'');
</ul>
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<ul> where suggested values for ''FullPathToMass'' are ''C:\Users\YourUserName\Documents\Matlab'' (Windows)or ''/home/YourUserName'' (LINUX). Of note, ''addpath'' does not permanently add ''FullPathToMass'' to Matlab's search folders (to add ''FullPathToMass'' permanently see below).</ul>
 
   
 
   
* Unpack now the zip archive ''pcode-microbems-v0xy.zip'' and copy all files into the new subdirectory ''...\mass''
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* To run MicrobeMS call the file ''mass.p'' by typing
 
* Start Matlab and enter at the command prompt
 
 
   
 
   
     >> edit pathdef  
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     >> mass
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* The license file ''genkey.gen'' is not included in the pcode installation archive. To register for a free license please send an e-mail with your name and the name of the institution you are working for to the address [mailto:lasch@microbe-ms.com lasch@microbe-ms.com]. In return, the license file genkey.gen will be emailed to you.
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* Copy the license key into the logfile directory (''DiaryDir'') of MicrobeMS ''C:\Users\YourUserName\Documents\Matlab'' (Windows) or ''/home/YourUserName'' (LINUX).
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* This procedure must be repeated each time
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    >> pathdef  
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The editor will now load the file ''pathdef.m''. Add a new line with the complete path to the MicrobeMS pcode toolbox
 
The editor will now load the file ''pathdef.m''. Add a new line with the complete path to the MicrobeMS pcode toolbox
</ul>
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     matlabroot,'\toolbox\matlab\mass;',...  
 
     matlabroot,'\toolbox\matlab\mass;',...  
 
* Save ''pathdef.m'' and restart Matlab
 
* Save ''pathdef.m'' and restart Matlab

Revision as of 15:56, 15 January 2020

Preface

MicrobeMS is a Matlab-based application which can be installed in two different versions (with basically the same functionality):

  • The stand-alone version requires installation of the MATLAB Compiler Runtime (MCR R2014a 64-bit).
  • MicrobeMS as a Matlab pcode toolbox. For this a licensed version of Matlab will be required.

Install MicrobeMS as a stand-alone application (Windows)

 

Prerequisites

MicrobeMS is Matlab based, so please verify that the MATLAB Compiler Runtime (MCR) is installed (MCR R2014a [8.3] Windows, 64-bit version). If the MCR is not installed, download the free Windows 64-bit version of the MCR for R2014a from the MathWorks website by navigating to

       http://www.mathworks.com/products/compiler/mcr/index.html

NOTE: To run the MCR installer administrator rights may be required. For further details please refer also to the section Specification of computer configuration.

 
Installation

  • Login with your Windows user account and download / unzip the MicrobeMS archive microbems.v.0XX.setup.zip (see Downloading MicrobeMS)
  • Start microbems.v.0XX.setup.exe and follow the instructions of the installation routine. During setup, you may be asked for the Windows administrator password.
  • The license file genkey.gen is not included in the installation package. To register for a free license please send an e-mail with your name and the name of the institution you are working for to the address lasch@microbe-ms.com
  • In return, the license file genkey.gen will be emailed to you. Copy the license key into the logfile directory of MicrobeMS (version 0.82, DiaryDir, C:\Users\Public\Documents\Matlab). In case of MicrobeMS versions before v. 0.82 the license key must be copied into the HomeDir of MicrobeMS (C:\Program files\MicrobeMS\MicrobeMS, default). Note that in some instances administrator rights may be required.

Installation of MicrobeMS as a Matlab pcode toolbox (Windows / Linux)

 
Prerequisites

Please note that Matlab R2014a, or newer, Matlabs's Statistics and Bioinformatics toolboxes are required when using MicrobeMS as a pcode toolbox. A complete 64-bit system consisting of 64-bit hardware, a Windows, or LINUX 64-bit operating system and Matlab 64-bit are highly recommended. For further details please refer also to Specification of computer configuration.

 
Installation  

  • It is recommended to create an additional subdirectory mass in the directory C:\Users\YourUserName\Documents\Matlab (Windows) or in the /home/YourUserName path (LINUX). Copy then all files into the new folder.
  • Start Matlab and enter at the command prompt
   >> addpath(FullPathToMass);
    where suggested values for FullPathToMass are C:\Users\YourUserName\Documents\Matlab (Windows)or /home/YourUserName (LINUX). Of note, addpath does not permanently add FullPathToMass to Matlab's search folders (to add FullPathToMass permanently see below).
  • To run MicrobeMS call the file mass.p by typing
   >> mass 
  • The license file genkey.gen is not included in the pcode installation archive. To register for a free license please send an e-mail with your name and the name of the institution you are working for to the address lasch@microbe-ms.com. In return, the license file genkey.gen will be emailed to you.
  • Copy the license key into the logfile directory (DiaryDir) of MicrobeMS C:\Users\YourUserName\Documents\Matlab (Windows) or /home/YourUserName (LINUX).
  • This procedure must be repeated each time
   >> pathdef 

The editor will now load the file pathdef.m. Add a new line with the complete path to the MicrobeMS pcode toolbox

   matlabroot,'\toolbox\matlab\mass;',... 
  • Save pathdef.m and restart Matlab
  • To run MicrobeMS call the file mass.p by typing
   >> mass 
  • The license file genkey.gen is not included in the installation package. To register for a free license please send an e-mail with your name and the name of the institution you are working for to the address lasch@microbe-ms.com
  • Don't forget to copy your personal license key genkey.gen into the directory {userpath}\Matlab (usually C:\User\YourUserName\Documents\Matlab, or alternatively into the toolbox directory ...\mass.

See also