jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified September 18, 2019
jpayne@69: 
jpayne@69: Description:  Runs TadpoleWrapper after some preprocessing,
jpayne@69: to allow optimal assemblies using long kmers.
jpayne@69: Only paired reads are supported.
jpayne@69: 
jpayne@69: Usage:
jpayne@69: tadpipe.sh in=reads.fq out=contigs.fa
jpayne@69: 
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>           Input reads.
jpayne@69: in2=<file>          Optional read 2, if reads are in two files.
jpayne@69: out=contigs.fa      Output file name.
jpayne@69: temp=$TMPDIR        Path to a directory for temp files.
jpayne@69: delete=t            Delete intermediate files.
jpayne@69: gz=f                Gzip intermediate files.
jpayne@69: 
jpayne@69: Other parameters can be passed to individual phases like this:
jpayne@69: 
jpayne@69: assemble_k=200,250  Set kmer lengths for assembly phase.
jpayne@69: merge_strict        Set the strict flag in merge phase.
jpayne@69: extend_el=120       Set the left-extension distance in the extension phase.
jpayne@69: 
jpayne@69: Valid prefixes:
jpayne@69: 
jpayne@69: filter_             PhiX and contaminant filtering.
jpayne@69: trim_               Adapter trimmming.
jpayne@69: merge_              Paired-read merging.
jpayne@69: correct_            Error correction.
jpayne@69: extend_             Read extension.
jpayne@69: assemble_           Final assembly.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx14g"
jpayne@69: z2="-Xms14g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 15000m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: tadpipe() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadPipe $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: tadpipe "$@"