icy-2.5.2-0.build.sh

#! /usr/bin/bash

set -eu

# ---------------------------------------------------------------- Preamble

PKG=icy
VERSION=2.5.2
BUILD=0

PREFIX=/pkg/icy-$VERSION-$BUILD
if [ -n "${TESTING:-}" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi

mkdir -p $PREFIX/bin
cd $PREFIX


cat > profile <<- EOF
	PATH=$PREFIX/bin:\$PATH
	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
EOF

# ----------------------------------------------------------------- Install

mkdir -p app
cd app

# orig: https://icy.bioimageanalysis.org/wp-content/uploads/2024/02/icy_2.5.2.tar.gz
BEEHIVE=https://beehive.molgen.mpg.de/f94861acd15245b01b57e24fc36c39a4/icy_2.5.2.tar.gz
wget -O- -nv $BEEHIVE | tar -xz --strip-components=2 --exclude='._*' --exclude='.DS*' --no-xattrs -f- 2>/dev/null

# dump the 'updating' start wrapper
mv icy icy.dist; chmod -c -x icy.dist


# the vtk-libs seem a bit weird, so straighten out a bit ...
rm -vrf lib/unix32
cd lib/unix64
rm -vf vtk.zip # it is also unpacked here ...
mkdir vtk      # this is needed
mv lib* vtk
cd vtk
# restore symlinks ... (who ever has created this archive, ...)
echo '# running ldconfig -xnv .'
ldconfig -xnv .


# ---------------------------------------------------------- Create startup

cd $PREFIX
sed -e "s,@PREFIX@,$PREFIX,g" > bin/icy <<- 'EOF'
	#! /usr/bin/bash
	
	set -eu
	
	# ----------------------------------------------- Make libraries accessible
	
	# Some vtk plugins refer to libawt.so
	if [ -z "${LIBAWTPATH:-}" ]; then
	  LIBAWTPATH=$(java -XshowSettings:properties --version 2>&1 | grep sun.boot.library.path)
	  LIBAWTPATH=${LIBAWTPATH#*sun.boot.library.path = }
	fi
	
	test -e "$LIBAWTPATH/libawt.so" || LIBAWTPATH=  # then not, at least we gave it a try ...
	
	LD_LIBRARY_PATH=@PREFIX@/lib/unix64/vtk${LIBAWTPATH:+:$LIBAWTPATH}${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
	# echo $LD_LIBRARY_PATH | tr ':' '\n' | nl
	
	export LD_LIBRARY_PATH
	
	# --------------------------------------------- Prepare local icy directory
	
	mkdir -pv $HOME/.local/Icy
	
	cd $HOME/.local/Icy
	
	# ----------------------------------------------- Handle possible leftovers
	
	if [ $# -gt 0 ]; then
	  if [ $1 = clean ]; then
	    rm -vf icy.run
	    shift
	  fi
	fi
	
	if [ -e icy.run ]; then
	
	  cat << EOM
	---------------------------------------------------------------------
	  Note:
	
	EOM
	
	  cat icy.run
	
	  cat << EOM
	
	  So it may be already running somewhere else, and you need to
	  close the application before you can proceed.
	
	  If icy or the machine crashed, you may need to remove.
	  $PWD/icy.run
	  
	    #> rm $PWD/icy.run
	
	  or start icy with
	  
	    #> icy clean
	
	---------------------------------------------------------------------
	EOM
	
	  exit
	
	fi
	
	echo "  icy started on host '$(hostname -s)', on $(date +%c)." >> icy.run
	
	
	# ---------------------------------------------------- Prepare fuse overlay
	
	# upper and workdir must be on the same file system (hmm, on NFS ...)
	
	UPPER=icy_user
	WORK=.fuse_transient
	LOWER=@PREFIX@
	MOUNTPOINT=icy_fmount
	
	mkdir -pv $UPPER $MOUNTPOINT $WORK
	
	if [ "$(stat -c %D $UPPER)" = "$(stat -c %D $MOUNTPOINT)" ] ; then
	  fuse-overlayfs \
	     -o lowerdir=$LOWER \
	     -o workdir=$WORK \
	     -o squash_to_uid=$UID \
	     -o squash_to_gid=$(id -g $UID) \
	     -o noacl \
	     -o upperdir=$UPPER \
	     $MOUNTPOINT
	else
	  if [ ! -e $MOUNTPOINT/app/icy.jar ]; then
	    echo "# ERROR: Something is wrong, can not find 'icy.jar'."
	    exit 1
	  fi
	fi
	
	# --------------------------------------------------------- Finally run icy
	
	cd icy_fmount/app
	java -jar icy.jar "$@"
	
	# ----------------------------------------------------------------- Tidy up
	
	cd $HOME/.local/Icy
	sleep 1
	fusermount -u $MOUNTPOINT
	rm icy.run || echo "# ERROR: Something is wrong, can not find 'icy.run' in $PWD."

EOF

chmod +x -c bin/icy

exit 0