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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified July 31, 2019
Description: Does nothing. Should be fast.
This is a template for making wrappers for new tools.
Usage: a_sample_mt.sh in=<input file> out=<output file>
Input may be fasta or fastq, compressed or uncompressed.
Standard parameters:
in=<file> Primary input, or read 1 input.
in2=<file> Read 2 input if reads are in two files.
out=<file> Primary output, or read 1 output.
out2=<file> Read 2 output if reads are in two files.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
a_sample_mt() {
local CMD="java $EA $EOOM $z -cp $CP templates.A_SampleMT $@"
echo $CMD >&2
eval $CMD
}
a_sample_mt "$@"
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