IGV 2.5: update to version 2.5.2

igv-2.5.2-0.build.sh

@@ -0,0 +1,151 @@
+#! /bin/bash
+
+# http://software.broadinstitute.org/software/igv/
+
+set -ex
+
+PKG=igv
+VERSION=2.5.2
+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
+cd $PREFIX
+mkdir -p attic
+
+if test -e attic/IGV_Linux_$VERSION.zip ; then
+  rm -vfr bin
+  mv attic/IGV_Linux_$VERSION.zip .
+  rm -vfr attic/*
+else
+  wget http://data.broadinstitute.org/igv/projects/downloads/$VERSION2/IGV_Linux_$VERSION.zip
+fi
+
+unzip IGV_Linux_$VERSION.zip
+
+mkdir -p attic
+mv IGV_Linux_$VERSION.zip attic
+
+mv IGV_Linux_$VERSION bin
+
+mv bin/readme.txt attic
+mv bin/igv* attic
+
+# trash the bundled jdk ("AdoptOpenJDK"/JAVA_VERSION="11.0.2")
+rm -fr bin/jdk-11
+
+cat >$PREFIX/profile <<-EOF
+	. /pkg/openjdk-11.0.3.2-0/profile
+	PATH=$PREFIX/bin:\$PATH
+	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
+EOF
+
+######################################################################
+# Setup our own startup scripts, and try to be smarter with the memory
+
+#############################  bin/igv  ##############################
+cat >bin/igv <<-'EOF'
+#!/bin/sh
+
+#-Xmx4g indicates 4 gb of memory, adjust number up or down as needed
+#Script must be in the same directory as igv.jar
+#Add the flag -Ddevelopment = true to use features still in development
+
+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 $MEM_GB -lt 4; then
+  MSG="#   This is fairly below the suitable amount of 4 GB.\n$CONSIDER"
+elif test $MEM_GB -gt 9 ; then
+  MSG="$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 5 seconds ...'
+  sleep 5
+fi
+
+prefix=`dirname \$(readlink \$0 || echo \$0)`
+exec java --module-path="${prefix}/lib" -Xmx4g \
+    @"${prefix}/igv.args" \
+    -Dsun.java2d.uiScale=1 \
+    -Dapple.laf.useScreenMenuBar=true \
+    -Djava.net.preferIPv4Stack=true \
+    --module=org.igv/org.broad.igv.ui.Main "$@"
+
+EOF
+
+chmod 755 bin/igv
+
+############################  bin/igvxmem  ###########################
+cat >bin/igvxmem <<-'EOF'
+#!/bin/sh
+
+#-Xmx4g indicates 4 gb of memory, adjust number up or down as needed
+#Script must be in the same directory as igv.jar
+#Add the flag -Ddevelopment = true to use features still in development
+
+MEM=4g
+
+case $1 in 
+  [1-9]g          |\
+  [1-9][0-9]g     |\
+  [1-2][0-9][0-9]g)
+                     MEM=$1
+                     shift
+  ;;
+
+  *)
+     echo "# Error: need a proper value for memory to use, eg. 8g"
+     exit 1
+  ;;
+esac
+
+prefix=`dirname \$(readlink \$0 || echo \$0)`
+exec java --module-path="${prefix}/lib" -Xmx$MEM \
+    @"${prefix}/igv.args" \
+    -Dsun.java2d.uiScale=1 \
+    -Dapple.laf.useScreenMenuBar=true \
+    -Djava.net.preferIPv4Stack=true \
+    --module=org.igv/org.broad.igv.ui.Main "$@"
+
+EOF
+
+chmod 755 bin/igvxmem
+
+############################  bin/igv.args  ##########################
+cat >bin/igv.args <<-'EOF'
+# Arguments to support JIDE on Java 11
+  --add-exports java.desktop/javax.swing.plaf.synth=jide.common
+  --add-exports java.desktop/sun.swing=jide.common
+  --add-exports java.desktop/sun.awt=jide.common
+  --add-exports java.desktop/sun.awt.image=jide.common
+  --add-exports java.desktop/sun.awt.shell=jide.common
+  --add-exports java.desktop/sun.awt.dnd=jide.common
+  --add-exports java.base/sun.security.action=jide.common
+
+# Disable a JAXB optimization that causes illegal access exceptions on Java 11
+  -Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize
+
+EOF
+
+chmod 644 bin/igv.args
+
+#############################   "HiDpi"   ###########################
+sed -e 's/uiScale=1/uiScale=2/' bin/igv > bin/igv_hidpi
+sed -e 's/uiScale=1/uiScale=2/' bin/igvxmem > bin/igvxmem_hidpi
+
+chmod 755 bin/igv_hidpi
+chmod 755 bin/igvxmem_hidpi
+
+exit