1.1.6. 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. Do the system check in the “Evaluate” stage. Try any recommendations 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 …

    • … installing binaries from online on Fedora, copy+paste:

      cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -package linux_openmp_64 -do_extras

    • … installing binaries from online on CentOS/RHEL 7, copy+paste:

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

    • … (alternative) installing already-downloaded binaries, you can use -local_package .. (replace “PATH_TO_FILE” with the actual path; also, if @update.afni.binaries has also been downloaded, you can skip the curl .. command), …:

      • … on Fedora, copy+paste:

        cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -local_package PATH_TO_FILE/linux_openmp_64.tgz -do_extras

      • … on CentOS/RHEL 7, copy+paste:

        cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -local_package PATH_TO_FILE/linux_centos_7_64.tgz -do_extras

    Purpose: Download and unpack the current binaries in your $HOME directory; set the AFNI binary directory name to $HOME/abin/; and add that location to the $PATH in both ~/.cshrc and ~/.bashrc.

  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.

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

    (To check your shell type, copy+paste: echo $0)

    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.

Setup Python (opt)

  1. AFNI has very minimal Python requirements—at present, matplotlib and numpy. For example, for the recommended automatic QC output from afni_proc.py, matplotlib is necessary.

    You can use any method to install+manage Python and its dependencies. But we note that we have found Miniconda to be convenient in managing Python environment(s), and it is replicatable across platforms. If you are interested, you can check out this tutorial, which has both verbose and quick instructions.

    But Miniconda is not required.

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. !Pro tip!: Bring a computer mouse to use at the Bootcamp. It is muuuuch easier to follow the demos that way.

  3. 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 ltr ls --color -ltr'   >> ~/.cshrc
echo 'alias ls="ls --color"'    >> ~/.bashrc
echo 'alias ll="ls --color -l"' >> ~/.bashrc
echo 'alias ltr="ls --color -ltr"' >> ~/.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.