.. _install_steps_linux_ubuntu18: **Linux, Ubuntu 18.04** =================================================================== .. contents:: The essential system setup :local: .. highlight:: none These setup instructions are for **Ubuntu Linux version 18.04** (Bionic Beaver). *And a note of thanks to Kiyotaka and other AFNI users who contributed advice to these instructions on the MB!* 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 & Install prerequisite packages ----------------------------- 1. 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 \ libcurl4-openssl-dev libxml2-dev \ libssl-dev libgfortran3 \ 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. #. 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``. 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 curl -O https://afni.nimh.nih.gov/pub/dist/src/scripts_src/@add_rcran_ubuntu_18.04.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_18.04.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_18.04.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 (of order an hour) to complete, because R will compile the packages. Sigh. #. If you are using Windows Subsystem Linux (WSL), and/or if your 'brms' package fails to install (as checked in the "Evaluation" step below), then consider to copy+paste:: sudo add-apt-repository -y "ppa:marutter/rrutter3.5" sudo add-apt-repository -y "ppa:marutter/c2d4u3.5" sudo apt update sudo apt install -y r-cran-rstan r-cran-shinystan r-cran-brms **Purpose:** Add a couple new repos from which to pull packages, and then get the desired R packages; these steps come mainly from `this helpful website `_. .. ---------- HERE/BELOW: copy for all installs -------------- Setup Python (opt) --------------------------------- .. include:: substep_miniconda.rst Prepare for Bootcamp -------------------- .. include:: substep_bootcamp.rst Evaluate setup/system (**important!**) ---------------------------------------- .. include:: substep_evaluate.rst Niceify terminal (optional, but goood) -------------------------------------- .. include:: substep_rcfiles.rst #. 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) ----------------------------------------------------------------- .. include:: substep_extra_packs.rst Keep up-to-date (remember!) --------------------------- .. include:: substep_update.rst