--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/splitribo.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,87 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified January 22, 2020
+
+Description:  Splits a file of various rRNAs into one file per type
+(16S, 18S, 5S, 23s).
+
+Usage:  splitribo.sh in=<file,file> out=<pattern>
+
+Standard parameters:
+in=<file>       Input file.
+out=<pattern>   Output file pattern, such as out_#.fa.  The # symbol is
+                required and will be substituted by the type name, such as
+                16S, to make out_16S.fa, for example.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+ziplevel=9      (zl) Set to 1 (lowest) through 9 (max) to change compression
+                level; lower compression is faster.
+
+types=16S,18S,5S,23S,m16S,m18S,p16S
+                Align to these sequences.  Fewer types is faster.  m16S
+                and m18S are mitochondrial; p16S is plastid (chloroplast).
+
+Processing parameters:
+minid=0.59      Ignore alignments with identity lower than this to a 
+                consensus sequences.
+refineid=0.70   Refine score by aligning to clade-specific consensus if
+                the best alignment to a universal consensus is below this.
+
+Java Parameters:
+-Xmx            This will set Java's memory usage, overriding autodetection.
+                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
+                specify 200 megs. The max is typically 85% of physical memory.
+-eoom           This flag will cause the process to exit if an out-of-memory
+                exception occurs.  Requires Java 8u92+.
+-da             Disable assertions.
+
+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="-Xmx4g"
+z2="-Xms4g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 42
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+mergeribo() {
+	local CMD="java $EA $EOOM $z -cp $CP prok.SplitRibo $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+mergeribo "$@"