#!/bin/sh


FASTQC_HOME=$BIRCH/java/FastQC

# The -dir switch is mainly for launching bioLegato from the birch launcher. By 
# prompting the user for a working folder, we help enforce good file organization
# habits.
if [ $# -gt 0 ]
then
   if [ ${1} = "-dir" ]
   then

      # Get rid of the -dir switch, and send the remaining command line arguments to bioLegato
      shift

      #Prompt the user to choose a working directory
      #CHANGEDIR=`java -cp "$BIRCH/script" DirChooser "Where do you want to work? Choose a folder."`
      CHANGEDIR=`java -jar $BIRCH/script/DirChooser2.jar "Where do you want to work? Choose a folder."`

      if [ -d "$CHANGEDIR" ]; then
	  cd "$CHANGEDIR"
      fi
   fi
fi


(perl $FASTQC_HOME/fastqc )&