Configuration HATSEQ

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  How to configure HATSEQ in Windows or an UNIX environment?

The installation of HATSEQ requires a x86-64 Windows or UNIX based system and 4GB memory or more is highly recommended.
Both platforms require the installation of MATLAB or the MATLAB Compiler Runtime (MCR) which is a standalone set of shared libraries that enable full functioning of HATSEQ.
The installation is described on the Installation page.


Windows x86-64 platform

  1. Download HATSEQ and the MCRinstaller file on the download page.
  2. Run the executable (HATSEQ_MCRinstaller.exe) and install the MATLAB Compiler Runtime.
  3. After the installation, add the MCR directory (<mcr_root>) to the environment variable by using DOS (3.1) or alternately Windows (3.2).
  For DOS, open a command prompt and issuing the DOS command: 
  set PATH=<mcr_root>\<version>\runtime\win64;%PATH%
     
  For R2012a the DOS-command is:
  set PATH=C:\Program Files\MATLAB\MATLAB Compiler Runtime\v717\runtime\win64;%PATH%
DOSscreenshot.png


  For Windows, add the PATH environment variable, by doing the following:
  1.    Select the My Computer icon on your desktop or in the "configuration" window.
  2.    Right-click the icon and select Properties from the menu.
  3.    Select the Advanced tab.
  4.    Click Environment Variables. 
  5.    Click "Edit" for variable "PATH"
  6.    Add the "<mcr_root>\<version>\runtime\win64" to the "PATH" (delimited by semi-colons ( ; ) )
  7.    Run HATSEQ by double-clicking on "HATSEQ.exe"
Step 1-2
Fig01-controlpanel.png
Arrow-right-big.png
Step 3
Fig02-System.png
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Step 4-6
Fig03-Environment variables.png

UNIX x86-64 platform

  1. After the installation, add the MCR directory (<mcr_root> with the <version> number) to the environment variable 
     by using "setenv" or the "export" function:
  
      setenv LD_LIBRARY_PATH 
      <mcr_root>/<version>/runtime/glnxa64: 
      <mcr_root>/<version>/bin/glnxa64: 
      <mcr_root>/<version>/sys/os/glnxa64: 
      <mcr_root>/version/sys/java/jre/glnxa64/jre/lib/amd64/native_threads: 
      <mcr_root>/<version>/sys/java/jre/glnxa64/jre/lib/amd64/server: 
      <mcr_root>/<version>/sys/java/jre/glnxa64/jre/lib/amd64: 
      setenv XAPPLRESDIR <mcr_root>/version/X11/app-defaults
  
      export LD_LIBRARY_PATH="<mcr_root>/<version>/runtime/glnxa64":
      "<mcr_root>/<version>/bin/glnxa64":
      "<mcr_root>/<version>/sys/os/glnxa64":
      "<mcr_root>/<version>/sys/java/jre/glnxa64/jre/lib/amd64/native_threads":
      "<mcr_root>/<version>/sys/java/jre/glnxa64/jre/lib/amd64/server":
      "<mcr_root>/<version>/sys/java/jre/glnxa64/jre/lib/amd64"
      export XAPPLRESDIR="<mcr_root>/<version>/X11/app-defaults"
  2. Run HATSEQ by issuing the command: "./HATSEQ"

MAC OS X platform

   To make the changes persistent after logout on Mac machines, add the MCR directory to the environment variable 
   DYLD_LIBRARY_PATH by issuing the setenv or export commands:
   Note that, <mcr_root> is the directory where MCR is installed on the target machine.
     SETENV example
     setenv DYLD_LIBRARY_PATH
         $DYLD_LIBRARY_PATH:
         <mcr_root>/v717/runtime/maci64:
         <mcr_root>/v717/sys/os/maci64:
         <mcr_root>/v717/bin/maci64:
         /System/Library/Frameworks/JavaVM.framework/JavaVM:
         /System/Library/Frameworks/JavaVM.framework/Libraries
     setenv XAPPLRESDIR <mcr_root>/v717/X11/app-defaults
   
   Example with the default installation path:
     setenv DYLD_LIBRARY_PATH
         $DYLD_LIBRARY_PATH:
         /Applications/MATLAB/MATLAB_Compiler_Runtime/v717/runtime/maci64:
         /Applications/MATLAB/MATLAB_Compiler_Runtime/v717/sys/os/maci64:
         /Applications/MATLAB/MATLAB_Compiler_Runtime/v717/bin/maci64:
         /System/Library/Frameworks/JavaVM.framework/JavaVM:
         /System/Library/Frameworks/JavaVM.framework/Libraries
     setenv XAPPLRESDIR /Applications/MATLAB/MATLAB_Compiler_Runtime/v717/X11/app-defaults
If "setenv" does not work, use "export" instead
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