--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/taxonomy.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,99 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified Jan 7, 2020
+
+Description:   Prints the full taxonomy of a string.
+String may be a gi number, NCBI taxID, or Latin name.
+An NCBI identifier should just be a number or ncbi|number.
+A gi number should be gi|number.
+Please read bbmap/docs/guides/TaxonomyGuide.txt for more information.
+Not: It is more convenient to use taxonomy.jgi-psf.org.
+
+Usage:  taxonomy.sh tree=<tree file> <identifier>
+Alternate usage: taxonomy.sh tree=<tree file> in=<file>
+
+Usage examples:
+taxonomy.sh tree=tree.taxtree.gz homo_sapiens canis_lupus 9606
+taxonomy.sh tree=tree.taxtree.gz gi=gitable.int1.d.gz in=refseq.fasta
+
+Processing parameters:
+in=<file>       A file containing named sequences, or just the names.
+out=<file>      Output file.  If blank, use stdout.
+tree=<file>     Specify a TaxTree file like tree.taxtree.gz.  
+                On Genepool, use 'auto'.
+gi=<file>       Specify a gitable file like gitable.int1d.gz. Only needed
+                if gi numbers will be used.  On Genepool, use 'auto'.
+accession=      Specify one or more comma-delimited NCBI accession to taxid
+                files.  Only needed if accesions will be used; requires ~45GB
+                of memory.  On Genepool, use 'auto'.
+level=null      Set to a taxonomic level like phylum to just print that level.
+minlevel=-1     For multi-level printing, do not print levels below this.
+maxlevel=life   For multi-level printing, do not print levels above this.
+silva=f         Parse headers using Silva or semicolon-delimited syntax.
+taxpath=auto    Set the path to taxonomy files; auto only works at NERSC.
+
+Parameters without an '=' symbol will be considered organism identifiers.
+
+* Note *
+Tree and table files are in /global/projectb/sandbox/gaag/bbtools/tax
+For non-Genepool users, or to make new ones, use taxtree.sh and gitable.sh
+
+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="-Xmx8g"
+z2="-Xms8g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 2000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+taxonomy() {
+	local CMD="java $EA $EOOM $z -cp $CP tax.PrintTaxonomy $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+taxonomy "$@"