1.1.5. Linux, Fedora and Red Hat

What to do?

These setup instructions are for modern Linux versions of Fedora (21+) and Red Hat (RHEL) 7, along with the corresponding CentOS 7.

  1. Each step involves either copy+pasting a command, or clicking on a download link.

  2. The user must have admin privileges (can run sudo ...). Some steps require an internet connection.

  3. Is your terminal shell bash or tcsh (or other)? To find out, type:

    echo $0
    
  4. Don’t forget the system check in the “Evaluate” stage. Try whatever the is recommended in its “Please Fix” section.

  5. If you run into any problems, please just ask a clear question on the Message Board.

  6. To open a text file, you can type gedit FILENAME. For example, to open the bash “rc” file:

    gedit ~/.bashrc &
    

Install prerequisite packages

  1. To be able to install latest packages, copy+paste:

    sudo yum update
    
  2. For ...

    • ... Fedora, copy+paste:

      sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc       \
                          PyQt4 R-devel netpbm-progs gnome-tweak-tool ed     \
                          xorg-x11-server-Xvfb firefox
      sudo yum update -y
      
    • ... CentOS/RHEL 7, copy+paste:

      sudo yum install -y epel-release
      sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc       \
                          PyQt4 R-devel netpbm-progs gnome-tweak-tool ed     \
                          libpng12 xorg-x11-server-Xvfb firefox
      sudo yum update -y
      
Purpose: Installs a lot of packages that AFNI depends on (so we don’t have to reinvent the wheel!).

Install AFNI binaries

  1. For ...

    • ... Fedora, copy+paste:

      cd
      curl -O https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries
      tcsh @update.afni.binaries -package linux_openmp_64 -do_extras
      
    • ... CentOS/RHEL 7, copy+paste:

      cd
      curl -O https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries
      tcsh @update.afni.binaries -package linux_centos_7_64 -do_extras
      

    Purpose: Download and unpack the current binaries in your $HOME directory (and yes, that @update* program works even, even though the link has “ubuntu” in it); set the AFNI binary directory name to $HOME/abin/; and add that location to the $PATH in both ~/.cshrc and ~/.bashrc.

    Note

    If the binary package has already been downloaded somewhere, instead of the above you can use -local_package with the location+name of the binary file, e.g.:

    tcsh @update.afni.binaries -local_package linux_openmp_64.tgz -do_extras
    
  2. Note if there is a copy+paste message in your terminal as the previous command finished. If so, follow it (so cryptic...).

Install R

  1. For ...

    • ... a tcsh terminal, copy+paste:

      setenv R_LIBS $HOME/R
      mkdir  $R_LIBS
      echo  'export R_LIBS=$HOME/R' >> ~/.bashrc
      echo  'setenv R_LIBS ~/R'     >> ~/.cshrc
      . ~/.cshrc
      
    • ... a bash terminal, copy+paste:

      export R_LIBS=$HOME/R
      mkdir  $R_LIBS
      echo  'setenv R_LIBS ~/R'     >> ~/.cshrc
      echo  'export R_LIBS=$HOME/R' >> ~/.bashrc
      . ~/.bashrc
      

    Purpose: Setup modern R from scratch. This relies on the environment variable $R_LIBS, to specify where to install the packages and where to read them from later (when R programs run). The last command sources the relevant RC file so the present terminal knows about the updates.

  2. Copy+paste:

    rPkgsInstall -pkgs ALL
    

    Purpose: Get specific R packages needed for AFNI programs. This step might take a while to complete.

Make AFNI/SUMA profiles

  1. Copy+paste:

    cp $HOME/abin/AFNI.afnirc $HOME/.afnirc
    suma -update_env
    

    Purpose: Set up vanilla-mode environment variables for AFNI and SUMA. To see how you can bend these to your will later, read the Technical notes.

Prepare for Bootcamp

  1. Copy+paste:

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

    Purpose: Download the Bootcamp class data; untar+unzip it (= open it up); move into the newly opened directory; execute a script to copy the files to $HOME/..

    If no errors occur in the above, and your afni_system_check.py says things are OK, you can delete/remove the tarred/zipped package, using “rm CD.tgz”. If you are really confident, you can also deleted the CD/ directory in the present location.

  2. Read+practice with the handy Unix documentation/tutorial.

    Purpose: give you a quick lesson/refresher on using basic Linux shell commands (e.g., ls, cd, less, etc.). It will greatly enhance your bootcamp experience– we promise!

Evaluate setup/system (important!)

  1. Copy+paste:

    afni_system_check.py -check_all
    
  2. Read the “Please Fix” section at the end. If there are no suggestions, then rejoice! Otherwise, try the suggestion(s) there.

  3. Open up the AFNI and SUMA GUIs, juuuust to make sure all is well:

    afni
    suma
    

    Report any crashes!

  4. If stuck, then ...

    • ... put any error message into an online search, and/or post a question on the Message Board

    • ... copy+paste this:

      afni_system_check.py -check_all > out.afni_system_check.txt
      

      ... and email the file “out.afni_system_check.txt” to an AFNI Guru for advice.

Niceify terminal (optional, but goood)

  1. To improve your life when using the terminal, copy+paste:

    echo 'set filec'    >> ~/.cshrc
    echo 'set autolist' >> ~/.cshrc
    echo 'set nobeep'   >> ~/.cshrc
    
    echo 'alias ls ls --color=auto' >> ~/.cshrc
    echo 'alias ll ls --color -l'   >> ~/.cshrc
    echo 'alias ls="ls --color"'    >> ~/.bashrc
    echo 'alias ll="ls --color -l"' >> ~/.bashrc
    

    Purpose: The first commands set up tab autocompletion for tcsh (which should already be enabled for bash, by default). The second set of commands make aliases so that different types of files (“normal” files, zipped files, executables, et al.) and directories are shown using different colors and boldness. It makes it much easier to navigate on a terminal, IMHO.

Keep up-to-date (remember!)

  1. To update your AFNI sometime, copy+paste:

    @update.afni.binaries -d
    

    That’s it!!

    Purpose: This will automatically download the correct, latest AFNI version to your computer, replacing your old binaries. It will also update the apearch help information. Update often!

  2. To check your AFNI version, copy+paste:

    afni -ver
    

    Purpose: Report this useful info whenever asking a question on the Message Board!

Note

The record of all changes (new options, new programs, bug fixes, et al.) in AFNI programs is maintained for all to see in the online AFNI History.