1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Written by Brian Bushnell 6Last modified October 17, 2016 7 8Description: Summarizes the output of multiple Quast reports for 9making box plots. 10 11Usage: summarizequast.sh */quast/report.tsv 12 13Parameters: 14out=stdout Destination for summary. 15required= A required substring in assembly names for filtering. 16normalize=t Normalize each metric to the average per report. 17box=t Print only 5 points per metric for box plots. 18 19Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 20" 21} 22 23#This block allows symlinked shellscripts to correctly set classpath. 24pushd . > /dev/null 25DIR="${BASH_SOURCE[0]}" 26while [ -h "$DIR" ]; do 27 cd "$(dirname "$DIR")" 28 DIR="$(readlink "$(basename "$DIR")")" 29done 30cd "$(dirname "$DIR")" 31DIR="$(pwd)/" 32popd > /dev/null 33 34#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 35CP="$DIR""current/" 36 37z="-Xmx400m" 38set=0 39 40if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 41 usage 42 exit 43fi 44 45calcXmx () { 46 source "$DIR""/calcmem.sh" 47 setEnvironment 48 parseXmx "$@" 49} 50calcXmx "$@" 51 52summarizequast() { 53 local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeQuast $@" 54# echo $CMD >&2 55 eval $CMD 56} 57 58summarizequast "$@" 59