Merge pull request #325 from mariux64/add-icy-2.5.2

icy-2.5.2: imageanalysis tool - add to repo

icy-2.5.2-0.build.sh

@@ -0,0 +1,163 @@
+#! /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