gatk.sh.in

#!/bin/sh

export LC_ALL=en_US.UTF-8

MEM_OPTS_SET_BY_USER="no"
for o in $@; do
  case $o in
    -X* )
      MEM_OPTS_SET_BY_USER="yes"
      ;;
  esac
done

if [ $MEM_OPTS_SET_BY_USER = "no" ]; then
  # memory options
  physmem_b=$(sysctl -n hw.physmem)
  physmem_mb=$((physmem_b/1024/1024))
  physmem_mb=$((physmem_mb*3/4)) # allow 3/4 of the memory
  #    -Xms<size>        set initial Java heap size
  #    -Xmx<size>        set maximum Java heap size
  MEM_OPTS="-Xms512m -Xmx${physmem_mb}m"
fi

# execute the command
%%JAVA%% $MEM_OPTS -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"