--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/randomgenome.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified October 17, 2019
+
+Description:  Generates a random, (probably) repeat-free genome.
+
+Usage:  randomgenome.sh len=<total size> chroms=<int> gc=<float> out=<file>
+
+Parameters:
+out=<file>      Output.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+len=100000      Total genome size.
+chroms=1        Number of pieces.
+gc=0.5          GC fraction.
+nopoly=f        Ban homopolymers.
+pad=0           Add this many Ns to contig ends; does not count toward 
+                genome size.
+seed=-1         Set to a positive number for deterministic output.
+amino=f         Produce random amino acids instead of nucleotides.
+includestop=f   Include stop codons in random amino sequences.
+
+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="-Xmx200m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+randomgenome() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.RandomGenome $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+randomgenome "$@"