#!/bin/bash
# ubuntuFixJogl2018.sh
# For Ubuntu 16.04 LTS
# Install Psychtoolbox from NeuroDebian, fix jogl install & matlab links
#
# Script based on proposed solution from Andreas Widmann
# for issue reported in:
# https://groups.yahoo.com/neo/groups/PSYCHTOOLBOX/conversations/topics/22674
#
# blame t.b.czuba 2018-02-09
# verify that the computer is running a Debian derivative
if ! command -v dpkg &> /dev/null; then
echo "this script is meant to be run on an Ubuntu system"
exit 1
fi
cd $HOME
# global variables
MATLABROOT="/usr/local/MATLAB/R2017b" # ...
TOOLROOT="$HOME/MLtoolbox"
echo "you are logged in as user $USER"
echo "matlab toolboxes will be installed in $TOOLROOT"
# configuration
################################################################################
# Add repositories for Psychtoolbox-3 installation (via NeuroDebian)
# - copy-pasta from 'all software' repository for Ubuntu 16.04
# - for different OS options see: http://neuro.debian.net/install_pkg.html?p=matlab-psychtoolbox-3-nonfree
wget -O- http://neuro.debian.net/lists/xenial.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
sudo apt update
# Install psychtoolbox
sudo apt install -y matlab-psychtoolbox-3-nonfree
# Add directories for Matlab toolboxes
sudo mkdir -v -m 777 "$TOOLROOT"
sudo chown -v "$USER":"$USER" "$TOOLROOT"
# symlink default PTB install location to ~/MLtoolbox
sudo ln -v -s /usr/share/psychtoolbox-3 $TOOLROOT/Psychtoolbox # def PTB location hardcoded by neurodebian
# Fix jogl errors in Matlab (as of Feb 7, 2018)
###################
# (1)
# ADD XENIAL-PROPOSED repository (necessary as of Feb. 2018)
sudo sh -c "echo 'deb http://archive.ubuntu.com/ubuntu/ \
xenial-proposed restricted main multiverse universe' \
> /etc/apt/sources.list.d/xenial-proposed.list"
sudo apt update -y
# ONLY INSTALL THE FOLLOWING from xenial-proposed!
# (...
sudo apt install -y libjogl2-java/xenial-proposed
# sudo apt install -y libjogl2-jni/xenial-proposed #...
# REMOVE XENIAL-PROPOSED repository
sudo rm /etc/apt/sources.list.d/xenial-proposed.list
sudo apt update -y
###################
# (2)
# Change the classpath.txt and librarypath.txt files in $MATLABROOT/toolbox/local.
#
# In classpath.txt find and comment or delete the following two lines (~line 450):
# $MATLABROOT/java/jarext/gluegen-rt.jar
# $MATLABROOT/java/jarext/jogl-all.jar
# and add instead:
# /usr/share/java/jogl2.jar
# /usr/share/java/gluegen2-rt.jar
#
# In librarypath.txt add at the end of the file (incl. a newline):
# /usr/lib/jni
###################
# (3)
# Now it should already work. To be sure that the MATLAB included libraries
# do not interfere I additionally renamed the following libraries in matlabroot/bin/glnxa64:
# libjogl_desktop.so
# libgluegen-rt.so
# libnativewindow_awt.so
# libnativewindow_X11.so
# which are now provided by the packages installed in (1).
cd $MATLABROOT/bin/glnxa64
sudo mv -v ./libjogl_desktop.so ./libjogl_desktop.so.bak
sudo mv -v ./libgluegen-rt.so ./libgluegen-rt.so.bak
sudo mv -v ./libnativewindow_awt.so ./libnativewindow_awt.so.bak
sudo mv -v ./libnativewindow_x11.so ./libnativewindow_x11.so.bak
#
# In matlabroot/toolbox/local/classpath I additionally renamed
# 3p_jogl.jcp
# to be shure it is not added back to classpath in case it is regenerated.
cd $MATLABROOT/toolbox/local/classpath
sudo mv -v ./3p_jogl.jcp ./3p_jogl.jcp.bak
printf "
###################
# PTB install & jogl error fix installed
###################
#
# Must manually apply the following edits w/in your Matlab installation
# To determine path to your \$MATLABROOT, fire up Matlab, then enter
# matlabroot
# in the command window.
#
###################
# Change the classpath.txt and librarypath.txt files in \$MATLABROOT/toolbox/local.
#
# In classpath.txt find and comment or delete the following two lines (~line 450):
# \$MATLABROOT/java/jarext/gluegen-rt.jar
# \$MATLABROOT/java/jarext/jogl-all.jar
# and add instead:
# /usr/share/java/jogl2.jar
# /usr/share/java/gluegen2-rt.jar
#
# In librarypath.txt add at the end of the file (incl. a newline):
# /usr/lib/jni
###################
"
