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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified August 18, 2016
Description: Generates multiple assemblies with Tadpole
to estimate the optimal kmer length.
Usage:
tadwrapper.sh in=reads.fq out=contigs%.fa k=31,62,93
Parameters:
out=<file> Output file name. Must contain a % symbol.
outfinal=<file> Optional. If set, the best assembly file
will be renamed to this.
k=31 Comma-delimited list of kmer lengths.
delete=f Delete assemblies before terminating.
quitearly=f Quit once metrics stop improving with longer kmers.
bisect=f Recursively assemble with the kmer midway between
the two best kmers until improvement halts.
expand=f Recursively assemble with kmers shorter or longer
than the current best until improvement halts.
All other parameters are passed to Tadpole.
"
}
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="-Xmx14g"
z2="-Xms14g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 15000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
tadwrapper() {
local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadpoleWrapper $@"
echo $CMD >&2
eval $CMD
}
tadwrapper "$@"
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