install

#!/bin/bash

# This script is shamelessly extended from https://github.com/saalfeldlab/n5-utils, thanks @axtimwalde & co!

USERTHREADS="-1"
USERMEM="-1"

while [[ $# -gt 0 ]]; do
  case $1 in
    -t|--threads)
      USERTHREADS="$2"
      shift # past argument
      shift # past value
      ;;
    -m|--mem)
      USERMEM="$2"
      shift # past argument
      shift # past value
      ;;
    -*|--*)
      echo "Unknown option $1"
      exit 1
      ;;
  esac
done

if [ $USERTHREADS == "-1" ]; then
  echo "You did not define the number of threads for Java/Spark can use, will be set automatically. You could do it by e.g.: './install -t 8' for 8 threads."
fi

if [ $USERMEM == "-1" ]; then
  echo "You did not define the memory that Java/Spark can use, will be set automatically. You could do it by e.g.: './install -m 64' for 64GB of RAM."
fi


if [ $USERMEM == "-1" ]; then
  # check for operating system
  if [[ "$OSTYPE" == "linux-gnu" ]]; then
    echo "Assuming on Linux operating system"
    MEM=$(cat /proc/meminfo | grep MemTotal | sed s/^MemTotal:\\\s*\\\|\\\s\\+[^\\\s]*$//g)
    MEMGB=$(($MEM/1024/1024))
    MEM=$((($MEMGB/5)*4))
  elif [[ "$OSTYPE" == "darwin"* ]]; then
    echo "Assuming on MacOS X operating system"
    # sysctl returns total hardware memory size in bytes
    MEM=$(sysctl hw.memsize | grep hw.memsize | sed s/hw.memsize://g)
    MEMGB=$(($MEM/1024/1024/1024))
    MEM=$((($MEMGB/5)*4))
  else
    echo "ERROR - Operating system (arg2) must be either linux or osx to determine max memory. Please specify max memory by e.g.: './install -m 64' for 64GB of RAM"
    exit
  fi

  echo "Available memory:" $MEMGB "GB, setting Java memory limit to" $MEM "GB"
else
  MEM=$USERMEM
  echo "Setting Java memory limit to" $MEM "GB"
fi

if [ $USERTHREADS == "-1" ]; then
  # check for operating system
  if [[ "$OSTYPE" == "linux-gnu" ]]; then
    if [ $USERMEM != "-1" ]; then
      echo "Assuming on Linux operating system"
    fi
    THREADS=$(nproc --all)
  elif [[ "$OSTYPE" == "darwin"* ]]; then
    if [ $USERMEM != "-1" ]; then
      echo "Assuming on MacOS X operating system"
    fi
    # sysctl returns number of physical cores
    THREADS=$(sysctl -n hw.ncpu)
  else
    echo "ERROR - Operating system (arg2) must be either linux or osx to determine number of physical cores. Please specify physical by e.g.: './install -t 8' to use 8 threads."
    exit
  fi
  echo "Available threads:" $THREADS", setting Java/Sparks threads accordingly."
else
  THREADS=$USERTHREADS
  echo "Setting Java/Spark number of threads to" $THREADS
fi


VERSION="2.1.1-SNAPSHOT"
INSTALL_DIR=$(pwd)
#INSTALL_DIR=${1:-$(pwd)}

echo ""
echo "Installing into $INSTALL_DIR (for local execution)"

echo 'Building the code'

sleep 2

mvn clean install
#echo 'Building a farjar, which can also be used for cluster/cloud execution' 
#mvn clean install -P fatjar
mvn -Dmdep.outputFile=cp.txt -Dmdep.includeScope=runtime dependency:build-classpath

# function that installs one command
# $1 - command name
# $2 - java class containing the functionality
install_command () {
	echo "Installing '$1' command into" $INSTALL_DIR

	echo '#!/bin/bash' > $1
	echo '' >> $1
	echo "JAR=\$HOME/.m2/repository/net/preibisch/BigStitcher/${VERSION}/BigStitcher-${VERSION}.jar" >> $1
	echo 'java \' >> $1
	echo "  -Xmx${MEM}g \\" >> $1
#	echo "  -Xmx${MEM}g -Dspark.master=local[${THREADS}] \\" >> $1
#	echo '  -XX:+UseConcMarkSweepGC \' >> $1
	echo -n '  -cp $JAR:' >> $1
	echo -n $(cat cp.txt) >> $1
	echo ' \' >> $1
	echo '  '$2' "$@"' >> $1

	chmod a+x $1
}

echo 'Installing BigStitcher ...'

install_command bigstitcher "net.preibisch.stitcher.plugin.BigStitcher"

# echo 'Installing utils ...'

#install_command downsample "net.preibisch.bigstitcher.spark.SparkDownsample"


if [ $(pwd) == "$INSTALL_DIR" ]; then
    echo "Installation directory equals current directory, we are done."
else
	echo "Creating directory $INSTALL_DIR and moving files..."
    mkdir -p $INSTALL_DIR
    mv affine-fusion $INSTALL_DIR/
fi

rm cp.txt

echo "Installation finished."