igv-2.4.14-0.build.sh

#! /bin/bash

# http://software.broadinstitute.org/software/igv/

set -e

PKG=igv
VERSION=2.4.14
VERSION2=$(echo $VERSION | cut -d. -f1,2)
BUILD=0

PREFIX=/pkg/$PKG-$VERSION-$BUILD
# PREFIX=/dev/shm/$PKG-$VERSION-$BUILD

mkdir -p $PREFIX
cd $PREFIX
mkdir -p attic

if test -e attic/IGV_$VERSION.zip ; then
  rm -vr bin
  mv attic/IGV_$VERSION.zip .
else 
  wget http://data.broadinstitute.org/igv/projects/downloads/$VERSION2/IGV_$VERSION.zip
fi

unzip IGV_$VERSION.zip

mkdir -p attic
mv IGV_$VERSION.zip attic

mv IGV_$VERSION bin

mv bin/readme.txt attic # this one lies!
mv bin/igv.sh attic
rm bin/igv.command

cat >$PREFIX/profile <<-EOF
	PATH=$PREFIX/bin:\$PATH
EOF

# try to be smarter with the memory

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 $MEM_GB -lt 4; then
  MSG="#   This is faily below the suitable amount of 4 GB.\n$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 -Xmx4g \
    -Dapple.laf.useScreenMenuBar=true \
    -Djava.net.preferIPv4Stack=true \
    -jar "$prefix"/lib/igv.jar "$@"

EOF

chmod 755 bin/igv

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 -Xmx$MEM \
    -Dapple.laf.useScreenMenuBar=true \
    -Djava.net.preferIPv4Stack=true \
    -jar "$prefix"/lib/igv.jar "$@"

EOF


chmod 755 bin/igvxmem