--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/taxserver.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,117 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell and Shijie Yao
+Last modified Jan 7, 2020
+
+Description:   Starts a server that translates NCBI taxonomy.
+
+Usage:  taxserver.sh tree=<taxtree file> table=<gitable file> port=<number>
+
+Usage examples:
+taxserver.sh tree=tree.taxtree.gz table=gitable.int1d.gz port=1234
+
+On Genepool:
+taxserver.sh tree=auto table=auto port=1234
+
+For accession number support, add accession=<something>  E.g.:
+
+External:
+taxserver.sh -Xmx45g tree=tree.taxtree.gz table=gitable.int1d.gz accession=prot.accession2taxid.gz,nucl_wgs.accession2taxid.gz port=1234
+
+On Genepool:
+taxserver.sh tree=auto table=auto accession=auto port=1234
+
+If all expected files are in some specific location, you can also do this:
+taxserver.sh -Xmx45g tree=auto table=auto accession=auto port=1234 taxpath=/path/to/files
+
+To kill remotely, launch with the flag kill=password, then access /kill/password
+
+Parameters:
+
+tree=auto           taxtree path.  Always necessary.
+table=auto          gitable path.  Necessary for gi number support.
+accession=null      Comma-delimited paths of accession files.
+                    Necessary for accession support.
+img=null            IMG dump file.
+pattern=null        Pattern file, for storing accessions more efficiently.
+port=3068           Port number.
+domain=             Domain to be displayed in the help message.
+                    Default is taxonomy.jgi-psf.org.
+dbname=             Set the name of the database in the help message.
+sketchcomparethreads=16    Limit compare threads per connection.
+sketchloadthreads=4 Limit load threads (for local queries of fastq).
+sketchonly=f        Don't hash taxa names.
+k=31                Kmer length, 1-32.  To maximize sensitivity and 
+                    specificity, dual kmer lengths may be used:  k=31,24
+prealloc=f          Preallocate some data structures for faster loading.
+
+Security parameters:
+
+killcode=           Set a password to allow remote killing.
+oldcode=            Set the password of a prior instance.
+oldaddress=         Attempt to kill a prior instance after initialization,
+                    by sending the old code to this address.  For example,
+                    taxonomy.jgi-psf.org/kill/
+allowremotefileaccess=f   Allow non-internal queries to use internal files
+                    for sketching in local mode.
+allowlocalhost=f    Consider a query internal if it originates from localhost
+                    without being proxied.
+addressprefix=128.  Queries originating from this IP address prefix will be
+                    considered internal.
+
+
+Unrecognized parameters with no = symbol will be treated as sketch files.
+Other sketch parameters such as index and k are also allowed.
+Please consult bbmap/docs/guides/TaxonomyGuide.txt and BBSketchGuide.txt for more information.
+
+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="-Xmx45g"
+z2="-Xms45g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+taxserver() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP tax.TaxServer $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+taxserver "$@"