install_NEURON.sh

#!/bin/bash
set -e

IVVER=18
NRNVER=r1059
XQVER=2.7.5
READLINE=/usr/local/opt/readline/
PYTHONBIN=/usr/bin/python

NRNDIR=/Applications/NEURON-$NRNVER

PROFILE=$HOME/.profile
source $PROFILE

#Check compilers
/usr/bin/clang --version
/usr/bin/python --version
/usr/bin/ruby --version

## Check if X11 is installed.
if [ ! -d /opt/X11 ]; then
    echo -e '\n\nXQuartz not found.'
#    echo -e 'XQuartz will be first installed and then you will be logged out.'
#    echo -e '\nPlease rerun this script after that.'
    echo -e "Downloading XQuartz.....\n"
    curl -LO http://xquartz.macosforge.org/downloads/SL/XQuartz-$XQVER.dmg
    hdiutil attach XQuartz-$XQVER.dmg
    echo -e '\n\nEnter the admin password if you are asked.'
    sudo installer -verboseR -pkg /Volumes/XQuartz-$XQVER/XQuartz.pkg -target /
    hdiutil detach /Volumes/XQuartz-$XQVER
    rm XQuartz-$XQVER.dmg
fi


## Check essential brew packages.
echo -e "\n\nInstalling essential homebrew packages..."

### readline
if [ ! -d $READLINE ]; then
  ## Check if homebrew is installed.
  if [ ! -f /usr/local/bin/brew ]; then
      echo -e "\n\nHomebrew not found. Installing homebrew..."
      ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

      touch $PROFILE
      echo -e '\n\nexport PATH=/usr/local/bin:$PATH' >> $PROFILE
      source $PROFILE
  fi
  
    echo -e "\n\nInstalling readline...\n"
    brew install readline
    READLINE=/usr/local/opt/readline/
fi

### Do we need gfortran? ###
# if [ ! -d $BREWCELLAR/gfortran ]; then
#     echo -e "\n\nInstalling gfortran...\n"
#     brew install gfortran
# fi

### openmpi
if [ ! -f /usr/local/bin/mpirun ]; then
  if [ ! -f /usr/local/bin/brew ]; then
      echo -e "\n\nHomebrew not found. Installing homebrew..."
      ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

      touch $PROFILE
      echo -e '\n\nexport PATH=/usr/local/bin:$PATH' >> $PROFILE
      source $PROFILE
  fi
    echo -e "\n\nInstalling openmpi...\n"
    brew install open-mpi
fi


## Get the sources.
echo -e "\n\nDownloading NEURON sources...\n"
curl -L -O http://raw2.github.com/shhong/CNS-starterpack/master/NEURON/NEURON.tar.gz 
tar zxvf NEURON.tar.gz

echo -e '\n\nNEURON will be installed in '$NRNDIR'.\n'

export CC='clang'
export OMPI_CC='clang'
export CXX='clang++'
export OMPI_CXX='clang++'
export CFLAGS='-Ofast -msse3 -Wno-return-type -Wno-implicit-function-declaration -Wno-implicit-int -fPIC'
export CXXFLAGS=$CFLAGS

## Compile and install IV
cd NEURON/iv
./configure --prefix=$NRNDIR/iv 
make -j4
make install
cd ..

## Compile and install NEURON
cd nrn
echo -e "Starting to compile NEURON...\n\n"
./configure --prefix=$NRNDIR/nrn --with-iv=$NRNDIR/iv --with-pic --with-nrnpython=$PYTHONBIN --with-paranrn --with-x --with-readline=$READLINE
make -j4
make install

### Compile and install nrnpython
echo -e '\n\nInstalling nrnpython module....\n'
cd src/nrnpython
python setup.py install
if [ $? -ne 0 ]; then { echo -e '\n\nFailed to install the python module. Now trying again with sudo...\n'; sudo python setup.py install; } fi
cd ../../../../

### Add the environment variables
touch $PROFILE
echo -e '\n\n## NEURON\nNEURON=/Applications/NEURON' >> $PROFILE
echo -e 'PLATFORM=x86_64\nexport DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$NEURON/iv/$PLATFORM/lib\nexport PATH=$NEURON/iv/$PLATFORM/bin:$PATH' >> $PROFILE
echo -e 'export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$NEURON/nrn/$PLATFORM/lib\nexport PATH=$NEURON/nrn/$PLATFORM/bin:$PATH' >> $PROFILE

## Clean up and quit
cd /Applications/
rm -rf NEURON
ln -s $NRNDIR NEURON

## Kick out the user and ask to come back again.
echo -e '\n\n\nAll done! Please log out and come back again.'
osascript -e 'tell application "System Events" to log out'