These instructions have moved to: HowTo Install AFNI




* If you have questions or difficulties, please ask on the AFNI message board.

* The commands in bold below are intended to be run with cut-and-paste,
to avoid any typos.


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Step 0: Install packages needed to run the shell and afni programs.
        Note that tcsh might not yet be on the system.

        This is system dependent, so choose one:
        
   Fedora 21 or 22:
      
      sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc   \
                          PyQt4 R-devel netpbm-progs gnome-tweak-tool ed
      sudo yum update -y
      


    Ubuntu 14.04:
      
      sudo apt-get install -y tcsh libxp6 xfonts-base python-qt4              \
                              r-base-dev libmotif4 libmotif-dev motif-clients \
                              gsl-bin netpbm gnome-tweak-tool libjpeg62
      sudo apt-get update
      



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Step 1: Now that tcsh is installed, set it as the default shell (if desired).
        Some subsequent instructions assume this shell.

      chsh -s /usr/bin/tcsh



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Step 2: Install AFNI.
        Assuming there is nothing yet on the system, this will install the
        AFNI binaries under $HOME/abin, update $path in the .cshrc file,
        and set up AFNI command tabbing.

   First get the install script:

      
      curl -O http://afni.nimh.nih.gov/pub/dist/bin/linux_fedora_21_64/@update.afni.binaries
      

   Then install the appropriate AFNI package.
   Note that most other Linux systems will probably work with linux_openmp_64.

      Fedora 21 or 22:

         tcsh @update.afni.binaries -package linux_fedora_21_64

      Ubuntu 14.04:

         tcsh @update.afni.binaries -package linux_openmp_64



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Step 3: Reboot.
        Consider a 'reboot' at this point.  That would deal with system
        updates, the change in login shell, and an updated path.

      reboot



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Step 4: Do a quick test to see that afni works.

      afni -ver

   If 'afni' does not work right away, or if 'reboot' was skipped, try
   starting a new tcsh shell and updating the path.

   If necessary:
      
      tcsh
      set path = ( $path ~/abin )
      rehash
      afni -ver
      

   The output of "afni -ver" should show something useful.


   Note: @update.afni.binaries should have set the path in ~/.cshrc.
         Verify this (set that the same 'set path' is in the file):

      cat ~/.cshrc



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Step 5: Install class data (if desired).
        Data is generally installed in the $HOME directory, so that it is
        easy to access during a class.

      
      curl -O http://afni.nimh.nih.gov/pub/dist/edu/data/CD.tgz
      tar xvzf CD.tgz
      cd CD
      tcsh s2.cp.files . ~
      cd ..
      

   If all goes well, delete the tgz package "rm CD.tgz".
   If you are *really* confidant, delete the CD tree.



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Step 6: Install current R libraries for the group analysis programs.
        This relies on the environment variable R_LIBS, which refers
        to a directory that will contain the R packages.  That variable
        should always be set, both to specify where to install the
        packages and where to read them from later (when running R
        programs).

      
      setenv R_LIBS $HOME/R
      mkdir $R_LIBS
      echo 'setenv R_LIBS ~/R' >> ~/.cshrc
      rPkgsInstall -pkgs ALL
      



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Step 7: Evaluate the setup.
        Create the .afnirc and .sumarc files, and evaluate the class
        setup using afni_system_check.py

        Run the check again just to see (or 'cat' the file).
        (we skip using 'tee' here)

      
      cp ~/abin/AFNI.afnirc ~/.afnirc
      suma -update_env
      afni_system_check.py -check_all > out.afni_system_check.txt

      afni_system_check.py -check_all