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view CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizecrossblock.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author | jpayne |
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date | Tue, 18 Mar 2025 17:55:14 -0400 |
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#!/bin/bash usage(){ echo " Written by Brian Bushnell Last modified June 10, 2016 Description: Summarizes CrossBlock results. Used for testing and validating CrossBlock. Usage: summarizecrossblock.sh in=<input file> out=<output file> Standard parameters: in=<file> A text file of files, or a comma-delimited list of files. Each is a path to results.txt output from Crossblock. out=<file> Output file for the summary. overwrite=f (ow) Set to false to force the program to abort rather than overwrite an existing file. Processing parameters: None yet! Java Parameters: -Xmx This will set Java's memory usage, overriding autodetection. -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. The max is typically 85% of physical memory. -eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java 8u92+. -da Disable assertions. Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. " } #This block allows symlinked shellscripts to correctly set classpath. pushd . > /dev/null DIR="${BASH_SOURCE[0]}" while [ -h "$DIR" ]; do cd "$(dirname "$DIR")" DIR="$(readlink "$(basename "$DIR")")" done cd "$(dirname "$DIR")" DIR="$(pwd)/" popd > /dev/null #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" CP="$DIR""current/" z="-Xmx200m" set=0 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then usage exit fi calcXmx () { source "$DIR""/calcmem.sh" setEnvironment parseXmx "$@" } calcXmx "$@" summarizecrossblock() { local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeCrossblock $@" echo $CMD >&2 eval $CMD } summarizecrossblock "$@"