--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/tadpipe.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified September 18, 2019
+
+Description:  Runs TadpoleWrapper after some preprocessing,
+to allow optimal assemblies using long kmers.
+Only paired reads are supported.
+
+Usage:
+tadpipe.sh in=reads.fq out=contigs.fa
+
+
+Parameters:
+in=<file>           Input reads.
+in2=<file>          Optional read 2, if reads are in two files.
+out=contigs.fa      Output file name.
+temp=$TMPDIR        Path to a directory for temp files.
+delete=t            Delete intermediate files.
+gz=f                Gzip intermediate files.
+
+Other parameters can be passed to individual phases like this:
+
+assemble_k=200,250  Set kmer lengths for assembly phase.
+merge_strict        Set the strict flag in merge phase.
+extend_el=120       Set the left-extension distance in the extension phase.
+
+Valid prefixes:
+
+filter_             PhiX and contaminant filtering.
+trim_               Adapter trimmming.
+merge_              Paired-read merging.
+correct_            Error correction.
+extend_             Read extension.
+assemble_           Final assembly.
+"
+}
+
+#This block allows symlinked shellscripts to correctly set classpath.
+pushd . > /dev/null
+DIR="${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="-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${RAM}m"
+}
+calcXmx "$@"
+
+tadpipe() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadPipe $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+tadpipe "$@"