package_mrtrix

#!/bin/bash
cat <<EOF
This script collates all the executables and runtime dependencies needed for
MRtrix3Tissue, and creates a GZ compressed archive suitable for deployment on
other systems. It takes all executables found in the bin/ folder and the mrtrix3
library from the lib/ folder. It is up to the user to ./configure and ./build
the software first.

       Stand-alone installation on systems without necessary dependencies
================================================================================

If the -standalone option is also supplied, this script will also attempt to
collate system libraries from the current system, allowing you to install onto
a target system without the necessary dependencies. This is particularly useful
for  installation on HPC systems and other centrally managed systems that often
run older distributions, and where users have little or no control over the
installation of required packages.

$ ./configure
$ ./build
$ ./package_mrtrix [-standalone]

EOF

echo -n "Press enter to proceed (or Ctrl-C to abort)..."
read

(
  echo - collating MRtrix3Tissue executables and mrtrix3 library...
  set -e
  mkdir -p _package/MRtrix3Tissue/
  cp -r bin/ _package/MRtrix3Tissue/
  cp -r lib/ _package/MRtrix3Tissue/ 
  cp -r share/ _package/MRtrix3Tissue/ 

  [ ${1:-"x"} == "-standalone" ] && (
    cat > _package/MRtrix3Tissue/launcher <<"EOF"
#!/bin/bash
PREFIX="$(dirname $0)/.."
COMMAND="$(basename $0)"
"$PREFIX"/lib/ld-*.so* "$PREFIX"/exe/"$COMMAND" "$@"
EOF
    chmod a+x _package/MRtrix3Tissue/launcher
    mkdir -p _package/MRtrix3Tissue/exe
    (
      cd _package/MRtrix3Tissue/bin
      for n in *; do
      file $n | grep -q script || ( 
        mv $n ../exe
        ln -s ../launcher $n
      )
      done
    )

    echo - collating dependent system libraries...
    LIBS=$(for n in bin/*; do ldd $n; done | sed 's/(.*)$//g' | sed 's/^.*=>//g' | sort | uniq | grep -v 'mrtrix\|vdso\|libGL.so\|libEGL.so\|nvidia\|fglrx' | xargs)
    echo '    libraries identified:'
    for n in $LIBS; do
      if [ -e $n ]; then
        echo '        '$n;
        cp $n _package/MRtrix3Tissue/lib/
      fi
    done

    QTCORE=$(for n in $LIBS; do echo $n; done | grep 'libQt.*Core')
    [[ $QTCORE ]] && ( # sort out Qt:
      [[ -z $QTPLUGDIR ]] && QTPLUGDIR=$(strings $QTCORE | sed -n 's/qt_plugpath=\(.*\)$/\1/p')
      [[ ! -d "$QTPLUGDIR" ]] && echo "could not find Qt plugins in $QTPLUGDIR, try 'export QTPLUGDIR=/usr/lib/qt/plugins/; package_mrtrix -standalone'" && exit 1
      echo '    Qt plugins in' $QTPLUGDIR
      LDD_PATTERN='^[[:space:]]*[[:graph:]]*[[:space:]]*=>[[:space:]]*\([[:graph:]]*\)[[:space:]]*([[:graph:]]*)$'
      QTLIBS=$(find $QTPLUGDIR -name '*.so' -print0 | xargs -n 1 -0 ldd | sed -n 's/'"$LDD_PATTERN"'/\1/p' | sort | uniq | grep -v 'libGL.so\|libEGL.so\|nvidia\|fglrx' )
      echo '    additional libraries required for Qt:'
      for n in $QTLIBS; do echo '        '$n; done

      cp $QTLIBS _package/MRtrix3Tissue/lib/
      cp -r $QTPLUGDIR _package/MRtrix3Tissue/lib/
      cat > _package/MRtrix3Tissue/lib/qt.conf << EOF
[Paths]
Prefix = .
EOF


    )

  )

) && cat <<EOF

You can now copy the folder _package/MRtrix3Tissue over to your target systems.
For example packing it up using:

$ cd _package
$ tar cfz MRtrix3Tissue.tar.gz MRtrix3Tissue

On your target system, unpack MRtrix3Tissue.tar.gz using:

$ tar xfz MRtrix3Tissue.tar.gz

You should also add the MRtrix3Tissue/bin to your PATH to finalise the installation.
EOF