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

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified December 19, 2018

Description:  Parses a webcheck log.
Input is expected to look like this:
Tue Apr 26 16:40:09 2016|https://rqc.jgi-psf.org/control/|200 OK|0.61

Usage:  webcheck.sh <input files>


Standard parameters:
in=<file>       Primary input.  Can use a wildcard (*) if 'in=' is omitted.
out=<file>      Summary output; optional.
fail=<file>     Output of failing lines; optional.
invalid=<file>  Output of misformatted lines; optional.
extendedstats=f (es) Print more stats.
overwrite=f     (ow) Set to false to force the program to abort rather than
                overwrite an existing file.

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="-Xmx1g"
set=0

if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
	usage
	exit
fi

calcXmx () {
	source "$DIR""/calcmem.sh"
	setEnvironment
	parseXmx "$@"
}
calcXmx "$@"

webcheck() {
	local CMD="java $EA $EOOM $z -cp $CP driver.ProcessWebcheck $@"
	echo $CMD >&2
	eval $CMD
}

webcheck "$@"