--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/fungalrelease.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,91 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified April 24, 2019
+
+Description:  Reformats a fungal assembly for release.
+Also creates contig and agp files.
+
+Usage:  fungalrelease.sh in=<input file> out=<output file>
+
+I/O parameters:
+in=<file>           Input scaffolds.
+out=<file>          Output scaffolds.
+outc=<file>         Output contigs.
+qfin=<file>         Optional quality scores input.
+qfout=<file>        Optional quality scores output.
+qfoutc=<file>       Optional contig quality scores output.
+agp=<file>          Output AGP file.
+legend=<file>       Output name legend file.
+overwrite=f         (ow) Set to false to force the program to abort rather than
+                    overwrite an existing file.
+
+Processing parameters:
+fastawrap=60        Wrap length for fasta lines.
+tuc=t               Convert sequence to upper case.
+baniupac=t          Crash on encountering a non-ACGTN base call.
+mingap=10           Expand all gaps (Ns) to be at least this long.
+mingapin=1          Only expand gaps that are at least this long.
+sortcscaffolds=t    Sort scaffolds descending by length.
+sortcontigs=f       Sort contigs descending by length.
+renamescaffolds=t   Rename scaffolds to 'scaffold_#'.
+scafnum=1           Number of first scaffold.
+renamecontigs=f     Rename contigs to 'contig_#' instead of 'scafname_c#'.
+contignum=1         Number of first contig; only used if renamecontigs=t.
+minscaf=1           Only retain scaffolds at least this long.
+mincontig=1         Only retain contigs at least this long.
+
+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 [[ $set == 1 ]]; then
+		return
+	fi
+}
+calcXmx "$@"
+
+fungalrelease() {
+	local CMD="java $EOOM $EA $EOOM $z $z2 -cp $CP jgi.FungalRelease $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+fungalrelease "$@"