.. from: https://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht00_inst/html/linux_inst_current.html .. _install_steps_linux_Fed: **Linux, Fedora** ========================================================== .. contents:: The essential system setup :local: .. highlight:: none These setup instructions are for modern **Linux versions** of **Fedora (21+)**. Things to note before starting -------------------------------- .. include:: substep_intro.rst #. **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 & Quick setup ---------------------------------- .. include:: substep_quickbuild_linux_Fed.rst (slow setup) Install prerequisite packages --------------------------------------------- 1. To be able to install latest packages, copy+paste:: sudo dnf update #. Copy+paste:: sudo dnf install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc \ PyQt4 R-devel netpbm-progs gnome-tweak-tool ed \ xorg-x11-server-Xvfb firefox \ python3-matplotlib python3-numpy \ python3-flask python3-flask-cors Copy+paste:: sudo dnf update -y **Purpose:** Installs a lot of packages that AFNI depends on (so we don't have to reinvent the wheel!). (slow setup) Install AFNI binaries --------------------------------------- 1. Choose one of the following approaches: * *(default) To install 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_openmp_64 -do_extras * *(alternative) To install already-downloaded binaries,* use ``-local_package ..`` (replacing ``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_openmp_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``. (slow setup) Install R -------------------------- 1. 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 . ~/.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:** Set the environment variable ``$R_LIBS`` to specify where to install+find the **R** packages. | #. 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 as R compiles packages. Sigh. .. ---------- HERE/BELOW: copy for all installs -------------- (slow setup) Prepare for Bootcamp ----------------------------------- .. include:: substep_bootcamp.rst (slow setup) Evaluate setup/system (**important!**) ----------------------------------------------------- .. include:: substep_evaluate.rst (slow setup) Niceify terminal (optional, but goood) --------------------------------------------------- .. include:: substep_rcfiles.rst (slow setup) Install extras (optional, but recommended for Bootcamp prep) ---------------------------------------------------------------------------- .. include:: substep_extra_packs.rst (slow setup) Keep up-to-date (remember!) ------------------------------------------------ .. include:: substep_update.rst A note on setting up Python/using Conda (opt) ----------------------------------------------- *For this OS, you should* not *need to do anything further to set up your Python*. .. include:: substep_miniconda.rst .. older, set term shell: Make "tcsh" default shell (optional/recommended) Copy+paste:: chsh -s /usr/bin/tcsh **Purpose:** Makes ``tcsh`` your default shell in the terminal. Reboot Copy+paste (to reboot):: reboot **Purpose:** This deals with system updates, any change in login shell, and path updates. .. comment: the OLD install R stuff for this version Install R --------- a. 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 using ``curl`` contains instructions to add a more uptodate set of R libraries to the source list.