annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizecrossblock.sh @ 69:33d812a61356

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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jpayne@69 1 #!/bin/bash
jpayne@69 2
jpayne@69 3 usage(){
jpayne@69 4 echo "
jpayne@69 5 Written by Brian Bushnell
jpayne@69 6 Last modified June 10, 2016
jpayne@69 7
jpayne@69 8 Description: Summarizes CrossBlock results.
jpayne@69 9 Used for testing and validating CrossBlock.
jpayne@69 10
jpayne@69 11 Usage: summarizecrossblock.sh in=<input file> out=<output file>
jpayne@69 12
jpayne@69 13 Standard parameters:
jpayne@69 14 in=<file> A text file of files, or a comma-delimited list of files.
jpayne@69 15 Each is a path to results.txt output from Crossblock.
jpayne@69 16 out=<file> Output file for the summary.
jpayne@69 17 overwrite=f (ow) Set to false to force the program to abort rather than
jpayne@69 18 overwrite an existing file.
jpayne@69 19
jpayne@69 20 Processing parameters:
jpayne@69 21 None yet!
jpayne@69 22
jpayne@69 23 Java Parameters:
jpayne@69 24 -Xmx This will set Java's memory usage, overriding autodetection.
jpayne@69 25 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
jpayne@69 26 The max is typically 85% of physical memory.
jpayne@69 27 -eoom This flag will cause the process to exit if an out-of-memory
jpayne@69 28 exception occurs. Requires Java 8u92+.
jpayne@69 29 -da Disable assertions.
jpayne@69 30
jpayne@69 31 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69 32 "
jpayne@69 33 }
jpayne@69 34
jpayne@69 35 #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69 36 pushd . > /dev/null
jpayne@69 37 DIR="${BASH_SOURCE[0]}"
jpayne@69 38 while [ -h "$DIR" ]; do
jpayne@69 39 cd "$(dirname "$DIR")"
jpayne@69 40 DIR="$(readlink "$(basename "$DIR")")"
jpayne@69 41 done
jpayne@69 42 cd "$(dirname "$DIR")"
jpayne@69 43 DIR="$(pwd)/"
jpayne@69 44 popd > /dev/null
jpayne@69 45
jpayne@69 46 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69 47 CP="$DIR""current/"
jpayne@69 48
jpayne@69 49 z="-Xmx200m"
jpayne@69 50 set=0
jpayne@69 51
jpayne@69 52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69 53 usage
jpayne@69 54 exit
jpayne@69 55 fi
jpayne@69 56
jpayne@69 57 calcXmx () {
jpayne@69 58 source "$DIR""/calcmem.sh"
jpayne@69 59 setEnvironment
jpayne@69 60 parseXmx "$@"
jpayne@69 61 }
jpayne@69 62 calcXmx "$@"
jpayne@69 63
jpayne@69 64 summarizecrossblock() {
jpayne@69 65 local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeCrossblock $@"
jpayne@69 66 echo $CMD >&2
jpayne@69 67 eval $CMD
jpayne@69 68 }
jpayne@69 69
jpayne@69 70 summarizecrossblock "$@"