1.1.4. Fedora and Red Hat Linux: The essential system setup¶
What to do?¶
Here we describe installation and system setup for reasonably modern Linux versions of Fedora (21+) and Red Hat (RHEL) 7, along with the corresponding CentOS 7.
- For each step, either:
- copy+paste commands from the green fields into the terminal (help and shortcuts here), or
- click on a link to download+install a package.
We assume the user has admin privileges (can run sudo ...
), and
some steps require an internet connection. Some steps depend on the OS
version.
To find out what shell you are using (e.g., bash
or tcsh
),
type:
echo $0
- IMPORTANT: Please:
- Do all steps.
- Run
afni_system_check.py -check_all
in the “Evaluate” stage. - And follow the system check recommendations in the output “Please Fix” section.
If anything seems problematic, please just ask a clear question on the Message Board.
Install prerequisite packages¶
For Fedora 21 (and higher), 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 sudo yum update -y
For 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 sudo yum update -y
Purpose: Installs a lot of packages that AFNI depends on (so we don’t have to reinvent the wheel!).
Make “tcsh” default shell (optional/recommended)¶
Copy+paste:
chsh -s /usr/bin/tcsh
Purpose: Makes tcsh
your default shell in the terminal.
Install AFNI binaries¶
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
Purpose: These commands: download and unpack the current binaries
into your $HOME
directory (and yes, that @update*
file works
even, even though it is in the “ubuntu” directory); 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, one can
use -local_package
, followed by the location+name of the
binary file, e.g.:
tcsh @update.afni.binaries -local_package linux_openmp_64.tgz -do_extras
Reboot¶
Copy+paste (to reboot):
reboot
Purpose: This deals with system updates, any change in login shell, and path updates.
Install R¶
Copy+paste the following:
for
tcsh
:setenv R_LIBS $HOME/R mkdir $R_LIBS echo 'setenv R_LIBS ~/R' >> ~/.cshrc curl -O https://afni.nimh.nih.gov/pub/dist/src/scripts_src/@add_rcran_ubuntu.tcsh sudo tcsh @add_rcran_ubuntu.tcsh
for
bash
:export R_LIBS=$HOME/R mkdir $R_LIBS echo 'export R_LIBS=$HOME/R' >> ~/.bashrc curl -O https://afni.nimh.nih.gov/pub/dist/src/scripts_src/@add_rcran_ubuntu.tcsh sudo tcsh @add_rcran_ubuntu.tcsh
Purpose: Setup modern R from scratch. This relies on the environment variable
$R_LIBS
, which specifies where to install the packages and where to read them from later (when R programs run). The file obtained usingcurl
contains instructions to add a more uptodate set of R libraries to the source list.Copy+paste the following:
rPkgsInstall -pkgs ALL
Purpose: Get specific R packages needed for AFNI programs.
Make AFNI/SUMA profiles¶
Copy+paste the following:
cp $HOME/abin/AFNI.afnirc $HOME/.afnirc
suma -update_env
Purpose: As noted in the Technical notes, AFNI and SUMA have a lot of default settings, controlled using environment variables. The above initializes vanilla-mode profiles with default values for both AFNI and SUMA.
These files ($HOME/.afnirc
and $HOME/.sumarc
) can be edited to
the user’s heart’s content, setting up specific profile features you
want when using AFNI and SUMA (e.g., having left=left when viewing
axial slices, making default colorbars, etc.).
Prepare for Bootcamp¶
Copy+paste the following:
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: In order, these commands: get the tarred+zipped directory
that contains the class data (and is hence named “CD”), downloading it
to the current location in the terminal; untar/unzip it (=opens it
up); go into the newly opened directory; execute a script to copy the
files to $HOME/CD/
; and finally exit the directory.
At this point, if there have been no errors, you can delete/remove
the tarred/zipped package, using “rm CD.tgz
”. If you are
really confident, you can also deleted the CD tree in the present
location (but leaving it in $HOME/CD/
).
Note
If using Linux terminal commands is new to you, then do look over the handy Unix documentation/tutorial and practice a few of the basic commands on your own system (e.g., ls, cd, less, etc.). It will greatly enhance your bootcamp experience– we promise!
Evaluate setup/system (important!)¶
Copy+paste the following, and read the displayed “Please Fix” section at the end of the output (try the suggestions there!):
afni_system_check.py -check_all
… and, for extra help, copy+paste this:
afni_system_check.py -check_all > out.afni_system_check.txt
and email the file “out.afni_system_check.txt” to your local AFNI Guru for advice.
Open up the AFNI and SUMA GUIs, juuuust to make sure all is well:
afni suma
Report any crashes!
If the “system check” gives any errors, please:
- check the list of known setup issues;
- search on the Message Board, and/or put the error into google;
- post a question on the aforementioned Message Board.
Niceify terminal (optional, but goood)¶
To improve your life when using the terminal, copy+paste these:
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
users 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!)¶
To update your AFNI any time in the future, just run:
@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!Check your AFNI version by typing:
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.