--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/fetchproks.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,70 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 19, 2019
+
+Description:  Writes a shell script to download one genome assembly
+and gff per genus or species, from ncbi.  Attempts to select the best assembly
+on the basis of contiguity.
+
+Usage:  fetchproks.sh <url> <outfile> <max species per genus: int> <use best: t/f>
+
+Examples:
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/bacteria/ bacteria.sh 2 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/archaea/ archaea.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/viral/ viral.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/protozoa/ protozoa.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/invertebrate/ invertebrate.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/fungi/ fungi.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/plant/ plant.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/ vertebrate_mammalian.sh 0 true
+fetchproks.sh ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_other/ vertebrate_other.sh 0 true
+
+Mitochondrion, plasmid, and plastid are different and use gbff2gff.
+
+Processing parameters:
+None yet!
+
+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="-Xmx1g"
+z2="-Xms1g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+fetchproks() {
+	local CMD="java $EA $EOOM $z -cp $CP prok.FetchProks $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+fetchproks "$@"