1.1.5. Linux, Ubuntu 20.04

What to do?

These setup instructions are for Ubuntu Linux version 20.04 (Focal Fossa). And a note of thanks to Chris Rorden, who contributed advice to these instructions!

  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. Copy+paste:

    sudo add-apt-repository universe
    
  2. Copy+paste:

    sudo apt-get update
    
    sudo apt-get install -y tcsh xfonts-base libssl-dev       \
                            python-is-python3                 \
                            python3-matplotlib                \
                            gsl-bin netpbm gnome-tweak-tool   \
                            libjpeg62 xvfb xterm vim curl     \
                            gedit evince eog                  \
                            libglu1-mesa-dev libglw1-mesa     \
                            libxm4 build-essential            \
                            libcurl4-openssl-dev libxml2-dev  \
                            libgfortran-8-dev libgomp1        \
                            gnome-terminal nautilus           \
                            gnome-icon-theme-symbolic         \
                            firefox xfonts-100dpi             \
                            r-base-dev
    

    Purpose: Installs a lot of packages that AFNI depends on (so we don’t have to reinvent the wheel!). This may take a little while to complete running.

    Some of these packages also improve terminal behavior, especially if you are running Ubuntu on a Windows machine.

  3. Copy+paste:

    sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19
    

    Purpose: Make a symbolic link for the specific version of GSL included in this version of Ubuntu.

Install AFNI binaries

  1. For …:

    • … (default) installing the binaries from online, copy+paste:

      cd
      curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
      tcsh @update.afni.binaries -package linux_ubuntu_16_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), 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_ubuntu_16_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
      
    • … 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
      

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

    Purpose: Step 1 of setting up modern R from scratch. Set the environment variable $R_LIBS to specify where to install+find the packages.

  2. Copy+paste:

    rPkgsInstall -pkgs ALL
    

    Purpose: Get specific R packages needed for AFNI programs. This step might take a while (of order an hour) to complete, because R will compile the packages. Sigh.

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.

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.

  2. Also, consider running gnome-tweak-tool and changing Windows -> Focus Mode from ‘click’ to ‘mouse’.

  3. Also, consider extending time for screen saver: System Settings -> Brightness & Lock, and set inactivity duration.

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.

Quick setup (condensed instructs)

This is a briefer form of the above setup instructions. It includes downloading the Bootcamp data and running the system check (so don’t forget to check that!).

There are 3 scripts to run. To download them, copy+paste:

cd
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_20_64_a_admin.txt
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_20_64_b_user.tcsh
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_20_64_c_nice.tcsh

Then run each of them, as described below. (Each creates a log file, for checking and/or asking questions.)

  1. To install packages requiring admin privileges (‘sudo’ password required)…

    • … From bash shell:

      sudo bash OS_notes.linux_ubuntu_20_64_a_admin.txt 2>&1 | tee o.ubu_20_a.txt
      
    • … From tcsh shell:

      sudo bash OS_notes.linux_ubuntu_20_64_a_admin.txt |& tee o.ubu_20_a.txt
      
    - show script y/n -

  2. To install other dependencies (don’t use ‘sudo’ here)…

    • … From bash shell:

      tcsh OS_notes.linux_ubuntu_20_64_b_user.tcsh 2>&1 | tee o.ubu_20_b.txt
      
    • … From tcsh shell:

      tcsh OS_notes.linux_ubuntu_20_64_b_user.tcsh |& tee o.ubu_20_b.txt
      
    - show script y/n -

  3. To niceify your terminal (optional, but useful)…

    • … From bash shell:

      tcsh OS_notes.linux_ubuntu_20_64_c_nice.tcsh 2>&1 | tee o.ubu_20_c.txt
      
    • … From tcsh shell:

      tcsh OS_notes.linux_ubuntu_20_64_c_nice.tcsh |& tee o.ubu_20_c.txt
      
    - show script y/n -