--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/tadwrapper.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,72 @@
+#!/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.
+"
+}
+
+#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${RAM}m"
+}
+calcXmx "$@"
+
+tadwrapper() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadpoleWrapper $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+tadwrapper "$@"