a script to download and compile all dependencies for MRtrix3 for installation on older distributions

install_from_source

#!/bin/bash

# to be used for installation on older systems when all else fails...
#
# Notes:
#
# - to prevent unnecessary downloads, dependencies are only fetched if the
#   'source_install_files' folder does not already exist. Delete it if you want to
#   fetch them again.
#
# - to prevent re-building the dependencies, they are only built if the 'lib64'
#   symbolic link is not present. Delete it if you need to build them again.
#
# - to prevent unnecessarily recompiling all of MRtrix3, the configure script
#   is only run if the 'config' file is absent. Delete it to force a reconfigure.



# set this to 1 to build Qt and mrview / shview:
BUILD_GUI=0

# any additional option to MRtrix3's configure script:
CONFIG_OPTIONS=""






if [ ! -f build -o ! -f build ]; then
  echo "Run this script from the MRtrix3 toplevel folder"
  exit 1
fi






if [ $BUILD_GUI -eq 0 ]; then
  CONFIG_OPTIONS="-nogui "$CONFIG_OPTIONS
fi
export NUMBER_OF_THREADS=$(getconf _NPROCESSORS_ONLN)

ROOT="$(pwd)"
LOG="${ROOT}/build_from_source.log"


set -e

function fetch {
  if [ -d "$1" ]; then 
    echo $1 already fetched - skipping
    return
  fi
  echo fetching $1 ...
  dir="$(mktemp -d)"
  (
    cd $dir
    wget -nv --show-progress "$2"
    tarball="$(ls)"
    echo unpacking $1 ...
    tar xf $tarball
    rm -f $tarball
  )
  mv "$dir/"* "$1"
  rmdir "$dir"
}



function compile {
  name="$1"
  if [ -f "${name}_installed" ]; then
    echo $1 already compiled and installed - skipping
    return 
  fi

  shift 
  echo building $name ...
  (
    cd "$name"
    eval "$@" &> "${LOG}"
    make -j ${NUMBER_OF_THREADS} &> "${LOG}"
    make install &> "${LOG}"
  )
  touch "${name}_installed"
}














mkdir -p source_install_files

if [ ! -L lib64 ]; then
  ln -s lib lib64
fi

export PATH="${ROOT}/bin:$PATH" 

(
  cd source_install_files

  fetch gcc ftp://ftp.gnu.org/gnu/gcc/gcc-5.5.0/gcc-5.5.0.tar.gz
  fetch zlib https://zlib.net/zlib-1.2.11.tar.gz
  fetch fftw ftp://ftp.fftw.org/pub/fftw/fftw-3.3.7.tar.gz
  fetch xz http://download.openpkg.org/components/cache/xz/xz-5.2.3.tar.gz
  fetch jpeg http://www.ijg.org/files/jpegsrc.v9c.tar.gz
  fetch tiff ftp://download.osgeo.org/libtiff/tiff-4.0.9.tar.gz
  fetch python3 https://www.python.org/ftp/python/3.5.2/Python-3.5.2.tgz
  fetch eigen3 http://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2

  # get GCC dependencies:
  if [ ! -L gcc/mpfr ] || [ ! -L gcc/gmp ] || [ ! -L gcc/mpc ]; then (
    cd gcc
    echo "fetching GCC prerequisites..."
    ./contrib/download_prerequisites
  )
  fi

  if [ $BUILD_GUI -gt 0 ]; then
    fetch qt5-base http://download.qt.io/official_releases/qt/5.9/5.9.4/submodules/qtbase-opensource-src-5.9.4.tar.xz
    fetch qt5-svg http://download.qt.io/official_releases/qt/5.9/5.9.4/submodules/qtsvg-opensource-src-5.9.4.tar.xz
  fi



  mkdir -p g++
  compile g++ ../gcc/configure --prefix="${ROOT}" -disable-multilib --enable-languages=c,c++

  # common environmemnt variables:
  export prefix="${ROOT}" CFLAGS="-isystem ${ROOT}/include" LDFLAGS="-L${ROOT}/lib"

  compile zlib ./configure
  compile fftw ./configure --prefix=${ROOT} --enable-shared
  compile xz ./configure --prefix=${ROOT} --enable-shared
  compile jpeg ./configure --prefix=${ROOT} --enable-shared
  compile tiff ./configure --prefix=${ROOT} --enable-shared
  compile python3 ./configure --prefix="${ROOT}"

  if [ $BUILD_GUI -gt 0 ]; then
    compile qt5-base ./configure -opensource -confirm-license --prefix=${ROOT} -no-openssl -qt-libpng -qt-xcb
    compile qt5-svg qmake
  fi
)




# build MRtrix3
export CXX=bin/g++ CFLAGS='-isystem /include' EIGEN_CFLAGS="-isystem source_install_files/eigen3/"

if [ ! -f config ]; then
  bin/python3 configure $CONFIG_OPTIONS
fi

bin/python3 build