igv: Add version 2.8.0

This install keeps windows (.bat) and mac (.command)
scripts, with proper env and JRE-11 available this igv
should be usable on these platforms too.

igv-2.8.0-0.build.sh

@@ -0,0 +1,104 @@
+#! /bin/bash
+
+# http://software.broadinstitute.org/software/igv/
+
+set -xe
+
+PKG=igv
+VERSION=2.8.0
+VERSION2=$(echo $VERSION | cut -d. -f1,2)
+BUILD=0
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
+
+mkdir -p $PREFIX
+cat >$PREFIX/profile <<-EOF
+	. /pkg/openjdk-11.0.3.2-0/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 $BUILDDIR
+
+test -e IGV_$VERSION.zip || wget http://data.broadinstitute.org/igv/projects/downloads/$VERSION2/IGV_$VERSION.zip
+test -d IGV_$VERSION || unzip -q IGV_$VERSION.zip
+
+find . -perm 775 -exec chmod 755 {} \+ -o -perm 664 -exec chmod 644 {} \+
+sed -e '/^exec/ s/Xmx4g/Xmx${IGVXMX:-8g}/' -i IGV_$VERSION/igv.sh
+sed -e '/^exec/ s/Xmx4g/Xmx${IGVXMX:-8g}/' -i IGV_$VERSION/igv_hidpi.sh
+
+mv IGV_$VERSION/* $PREFIX
+rmdir IGV_$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=$(grep 'MemTotal:' /proc/meminfo | head -1 | rev | cut -d' ' -f2 | rev)
+	MEM_GB=$(( $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
+
+
+exit