1.1.3. Linux, Ubuntu 16.04 - 17.10¶

The essential system setup

Things to note before starting
Install prerequisite packages
Install AFNI binaries
Install R
Setup Python (opt)
Prepare for Bootcamp
Evaluate setup/system (important!)
Niceify terminal (optional, but goood)
Install extras (optional, but recommended for Bootcamp prep)
Keep up-to-date (remember!)

These setup instructions are for Ubuntu Linux versions 16.04 (Xenial Xerus) through 17.10 (Artful Aardvark).

Things to note before starting ¶

Each step involves either copy+pasting a command, or clicking on a download link.
Admin privileges are needed for some steps: check if you can run sudo ls, entering the correct password. If you can’t, perhaps ask an administrator to do that step, and you can do the others that don’t require it.
Note your terminal shell type (bash, zsh, tcsh, csh, etc.), by copy+pasting:
```
echo $0
```
Do the system check in the “Evaluate” stage. Try any recommendations in its “Please Fix” section.
If you run into any problems, please just ask a clear question on the AFNI Message Board.
To copy and paste in a Linux terminal, one can use Ctrl+Shift+c and Ctrl+Shift+v, respectively. (In WSL terminals, one might first enable this functionality: rightclick on the panel’s taskbar, select “Properties” and put a checkmark by this option.)
To open a text file, use any text editor you like, and/or you can type gedit FILENAME, such as either:
```
gedit ~/.bashrc

gedit ~/.bashrc &
```

Install prerequisite packages ¶

Copy+paste:
```
sudo add-apt-repository universe
```

Copy+paste:

sudo apt-get update

Copy+paste:

sudo apt-get install -y tcsh xfonts-base python-qt4       \
                        python-matplotlib                 \
                        gsl-bin netpbm gnome-tweak-tool   \
                        libjpeg62 xvfb xterm vim curl     \
                        gedit evince eog                  \
                        libglu1-mesa-dev libglw1-mesa     \
                        libxm4 build-essential            \
                        gnome-terminal nautilus           \
                        gnome-icon-theme-symbolic         \
                        firefox xfonts-100dpi

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.

Install AFNI binaries ¶

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.

Install R ¶

Check your shell type (echo $0). 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
curl -O https://afni.nimh.nih.gov/pub/dist/src/scripts_src/@add_rcran_ubuntu.tcsh

… 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
curl -O https://afni.nimh.nih.gov/pub/dist/src/scripts_src/@add_rcran_ubuntu.tcsh

Purpose: Step 1 of setting up modern R from scratch. Set the environment variable $R_LIBS to specify where to install+find the packages. The file obtained using curl contains instructions to add a more uptodate set of R libraries to the source list.

Copy+paste:
```
sudo tcsh @add_rcran_ubuntu.tcsh
```
Purpose: This script updates your package manager to be able to get a modern version of R. If you don’t already have R on your system, it will install it. If you do have R, it will stop and ask if you want to remove it and update it, or not.
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)¶

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. In fact, your OS might have all the Python+modules needed to run AFNI already. Check this by running:

afni_system_check.py -check_all

... and seeing there are no notes in the “Please fix” section at the end—if there are none about Python, then you are all set!

But if you do still need to setup Python with appropriate modules, or you want to manage different environments with different package needs (Python or otherwise), then we note that we have found Miniconda to be convenient. It is cross-platform (with occasional OS-specific quirks). If you are interested in either using it or reading more about it, you can check out this tutorial, which has both verbose and quick instructions.

But Miniconda is not required.

Prepare for Bootcamp ¶

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

Copy+paste:
```
afni_system_check.py -check_all
```
Read the “Please Fix” section at the end. If there are no suggestions, then rejoice! Otherwise, try the suggestion(s) there.
Open up the AFNI and SUMA GUIs, juuuust to make sure all is well:
```
afni
suma
```
Report any crashes!
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)¶

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.
Also, consider running gnome-tweak-tool and changing Windows -> Focus Mode from ‘click’ to ‘mouse’.
Also, consider extending time for screen saver: System Settings -> Brightness & Lock, and set inactivity duration.

Install extras (optional, but recommended for Bootcamp prep)¶

If you plan to use the FATCAT_matplot functionality in AFNI, then copy+paste the following:
```
@afni_R_package_install -shiny -circos
```
Purpose: This script will install the R packages for FATCAT_matplot and other ‘shiny’ tools (via bioconductor). And it might take a little while to complete…

Keep up-to-date (remember!)¶

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!
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.