MZmine Linux startup script

MZmine

#!/bin/bash

# Enhanced Linux MZmine startup script, works as symbolic link.


# The HEAP_SIZE variable defines the Java heap size in MB. 
# That is the total amount of memory available to MZmine 2.
# By default we set this to the half of the physical memory 
# size, but feel free to adjust according to your needs. 
HEAP_SIZE=`free -m | awk '/Mem:/ {print int($2 / 2)}'`

# The TMP_FILE_DIRECTORY parameter defines the location where temporary 
# files (parsed raw data) will be placed. Default is /tmp.
TMP_FILE_DIRECTORY=/tmp

# Set R environment variables.
export R_HOME=/usr/lib64/R
export R_SHARE_DIR=/usr/share/R/share 
export R_INCLUDE_DIR=/usr/share/R/include
export R_DOC_DIR=/usr/share/R/doc
export R_LIBS_USER=${HOME}/R/x86_64-pc-linux-gnu-library/2.10

# Include R shared libraries in LD_LIBRARY_PATH.
export LD_LIBRARY_PATH=${R_HOME}/lib:${R_HOME}/bin

# The directory holding the JRI shared library (libjri.so).
JRI_LIB_PATH=${R_LIBS_USER}/rJava/jri

# It is usually not necessary to modify the JAVA_COMMAND parameter, but 
# if you like to run a specific Java Virtual Machine, you may set the 
# path to the java command of that JVM.
JAVA_COMMAND=java

# It is not necessary to modify the following section
JAVA_PARAMETERS="-XX:+UseParallelGC -Djava.io.tmpdir=$TMP_FILE_DIRECTORY $USE_64_BIT -Xms${HEAP_SIZE}m -Xmx${HEAP_SIZE}m -Djava.library.path=${JRI_LIB_PATH}"
CLASS_PATH=lib/MZmine-2.10.jar
MAIN_CLASS=net.sf.mzmine.main.MZmineCore

# Make sure we are in the correct directory
SOURCE="${BASH_SOURCE[0]}"
app_dir="$( dirname "$SOURCE" )"
while [ -h "$SOURCE" ]
do
  SOURCE="$(readlink "$SOURCE")"
  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
  app_dir="$( cd -P "$( dirname "$SOURCE"  )" && pwd )"
done
app_dir="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SCRIPTDIR=$app_dir
cd "$SCRIPTDIR"

# Show java version, in case a problem occurs
echo "-version" | xargs $JAVA_COMMAND

# This command starts the Java Virtual Machine
echo "$JAVA_PARAMETERS" -classpath $CLASS_PATH $MAIN_CLASS "$@" | xargs $JAVA_COMMAND