igv: add version 2.17.1

See  https://openjdk.org/jeps/261 for the '--add-exports' fix
in igv.args

igv-2.17.1-0.build.sh

@@ -0,0 +1,123 @@
+#! /bin/bash
+
+# http://software.broadinstitute.org/software/igv/
+
+## https://data.broadinstitute.org/igv/projects/downloads/2.17/IGV_2.17.1.zip
+
+set -xe
+
+PKG=igv
+VERSION=2.17.1
+BUILD=0
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$USER/$PKG-$VERSION-$BUILD ; fi
+
+mkdir -p $PREFIX
+cat >$PREFIX/profile <<-EOF
+	. /pkg/openjdk-21.0.0.35-0/profile
+	PATH=$PREFIX:\$PATH
+	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
+EOF
+. $PREFIX/profile
+
+BUILDDIR=$PREFIX/build
+
+mkdir -p $BUILDDIR
+cd $BUILDDIR
+
+BEEHIVE=https://beehive.molgen.mpg.de/03ac0b25031175a2a6c3f01a7990c3ce/IGV_2.17.1.zip
+test -e IGV_$VERSION.zip || wget -nv $BEEHIVE
+test -d IGV_$VERSION || bsdtar -xf IGV_$VERSION.zip
+
+mv IGV_$VERSION/* $PREFIX
+# intentionally fail if not empty
+rmdir IGV_$VERSION
+
+cd $PREFIX
+cat >igv <<-'EOF'
+	#!/bin/sh
+	
+	die() { echo $1; exit 1; }
+	
+	parse_mem() {
+	  case $1 in
+	    [1-9]g | [1-9][0-9]g | [1-2][0-9][0-9]g)
+	      IGVXMX=$1 ;;
+	    *)
+	      die "# Error: need a proper value for memory to use, eg. 8g" ;;
+	  esac
+	}
+	
+	script=`basename $0`
+	
+	IGVXMX=${IGVXMX:-8g}
+	export IGVXMX
+	
+	case "$script" in
+	  igvxmem_hidpi)
+	     parse_mem $1; shift
+	     exec igv_hidpi.sh "$@" ;;
+	  igvxmem)
+	     parse_mem $1; shift
+	     exec igv.sh "$@" ;;
+	esac
+	
+	MEM_KB=$(grep -m1 'MemTotal:' /proc/meminfo | rev | cut -d' ' -f2 | rev)
+	MEM_GB=$(( $MEM_KB/1024/1024 ))
+	
+	CONSIDER="#   Consider using 'igvxmem XYZg' to start igv with proper memory setup."
+	
+	if test $MEM_GB -lt 7; then
+	  MSG="#   This is fairly below the suitable amount of 8 GB.\n$CONSIDER"
+	elif test $MEM_GB -gt 17 ; then
+	  MSG="$CONSIDER\n#   To gain better performance you may increase the memory in sane steps."
+	fi
+	
+	if test -n "$MSG"; then
+	  echo '# NOTE:'
+	  echo "#   found approx. $MEM_GB GB of Memory on your host."
+	  echo '#'
+	  echo -e "$MSG"
+	  echo '#'
+	  echo '# igv with default settings will start in 3 seconds ...'
+	  sleep 3
+	fi
+	
+	case "$script" in
+	  igv_hidpi)
+	     exec igv_hidpi.sh "$@" ;;
+	  *)
+	     exec igv.sh "$@" ;;
+	esac
+	
+EOF
+
+chmod 755 igv
+
+ln -s igv igvxmem
+ln -s igv igv_hidpi
+ln -s igv igvxmem_hidpi
+
+
+# delivered igv.args are not up to date, yielding several disturbing warnings like
+# WARNING: Unknown module: jide.common specified to --add-exports, fix it ...
+
+cat >igv.args <<- EOF
+
+	# from https://openjdk.org/jeps/261
+	# The --add-exports and --add-opens options must be used with great care.
+	# You can use them to gain access to an internal API of a library module
+
+	--add-exports java.desktop/javax.swing.plaf.synth=ALL-UNNAMED
+	--add-exports java.desktop/sun.swing=ALL-UNNAMED
+	--add-exports java.desktop/sun.awt=ALL-UNNAMED
+	--add-exports java.desktop/sun.awt.image=ALL-UNNAMED
+	--add-exports java.desktop/sun.awt.shell=ALL-UNNAMED
+	--add-exports java.desktop/sun.awt.dnd=ALL-UNNAMED
+	--add-exports java.base/sun.security.action=ALL-UNNAMED
+
+EOF
+
+
+exit