--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/runhmm.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified August 5, 2020
+
+Description:  Processes data.  (WIP)
+
+Usage:  runhmm.sh in=<file> out=<file>
+
+Parameters and their defaults:
+
+ow=f                    (overwrite) Overwrites files that already exist.
+
+Processing Parameters:
+
+None yet!
+
+
+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="-Xmx300m"
+z="-Xms300m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+function runhmm() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP hmm.HMMSearchReport $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+runhmm "$@"