spark_custom_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


VERSION="0.0.2-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 fatjar, which can also be used for cluster/cloud execution' 
mvn clean install -P fatjar -Dmaven.repo.local=/opt/BigStitcher-Spark/repo
mvn -Dmdep.outputFile=cp.txt -Dmdep.includeScope=runtime dependency:build-classpath -Dmaven.repo.local=/opt/BigStitcher-Spark/repo


# 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 '' >> $1
    echo 'if [ "$#" -lt 2 ]; then echo "Usage: $0 <mem_gb> <threads> <other parameters (enter in mem_gb and threads to see usage)>"; exit 1; fi' >> $1
    echo 'MEM=$1' >> $1
    echo 'THREADS=$2' >> $1
    echo 'shift 2' >> $1
    echo "JAR=/opt/BigStitcher-Spark/repo/net/preibisch/BigStitcher-Spark/${VERSION}/BigStitcher-Spark-${VERSION}.jar" >> $1
    echo 'java \' >> $1
    echo '  -Xmx${MEM}g -Dspark.master=local[${THREADS}] \' >> $1
    echo -n '  -cp $JAR:' >> $1
    echo -n $(cat cp.txt) >> $1
    echo ' \' >> $1
    echo '  '$2' "$@"' >> $1

    chmod a+x $1
}

echo 'Installing workflow tools ...'

install_command resave "net.preibisch.bigstitcher.spark.SparkResaveN5"
install_command detect-interestpoints "net.preibisch.bigstitcher.spark.SparkInterestPointDetection"
install_command match-interestpoints "net.preibisch.bigstitcher.spark.SparkGeometricDescriptorMatching"
install_command stitching "net.preibisch.bigstitcher.spark.SparkPairwiseStitching"
install_command solver "net.preibisch.bigstitcher.spark.Solver"
install_command affine-fusion "net.preibisch.bigstitcher.spark.SparkAffineFusion"
install_command nonrigid-fusion "net.preibisch.bigstitcher.spark.SparkNonRigidFusion"

echo 'Installing utils ...'

install_command downsample "net.preibisch.bigstitcher.spark.SparkDownsample"
install_command clear-interestpoints "net.preibisch.bigstitcher.spark.ClearInterestPoints"
install_command clear-registrations "net.preibisch.bigstitcher.spark.ClearRegistrations"
install_command transform-points "net.preibisch.bigstitcher.spark.TransformPoints"


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."