--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/gi2taxid.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,97 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell.
+Last modified December 19, 2019
+
+Description:  Renames sequences to indicate their NCBI taxIDs.
+The headers must be in NCBI or Silva format with gi numbers,
+accessions, or organism names.  Only supports fasta and gff files.
+
+Usage:  gi2taxid.sh in=<file> out=<file> server
+
+Parameters:
+in=<file>       Input sequences; required parameter.  Must be fasta.
+                This can alternatively be a comma-delimited list,
+                or just a bunch of space-delimited filenames, e.g.:
+                gi2taxid.sh x.fa y.fa z.fa out=tid.fa tree=auto table=auto
+out=<file>      Destination for renamed sequences.
+invalid=<file>  Destination for headers with no taxid.
+keepall=t       Keep sequences with no taxid in normal output.
+prefix=t        Append the taxid as a prefix to the old header, but keep
+                the old header.
+title=tid       Set the title of the new number (e.g. ncbi, taxid, tid).
+ziplevel=2      (zl) Compression level for gzip output.
+pigz=t          Spawn a pigz (parallel gzip) process for faster 
+                compression than Java.  Requires pigz to be installed.
+silva=f         Parse headers in Silva format.
+shrinknames=f   Replace multiple concatenated headers with the first.
+deleteinvalid=f Delete the output file if there are any invalid headers.
+
+Taxonomy file flags:
+server=f        Use the taxonomy server instead of local files.
+                Server mode only works for accessions (like RefSeq).
+tree=           Specify a taxtree file.  On Genepool, use 'auto'.
+gi=             Specify a gitable file.  On Genepool, use 'auto'.
+accession=      Specify one or more comma-delimited NCBI accession to
+                taxid files.  On Genepool, use 'auto'.
+
+Java Parameters:
+-Xmx            This will set Java's memory usage, overriding autodetection.
+                -Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 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/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""
+
+z="-Xmx7g"
+z2="-Xms7g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 7000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+
+gi2taxid() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP tax.RenameGiToTaxid $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+gi2taxid "$@"