1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell.
6Last modified Jan 7, 2020
7
8Description:  Creates tree.taxtree from names.dmp and nodes.dmp.
9These are in taxdmp.zip available at ftp://ftp.ncbi.nih.gov/pub/taxonomy/
10The taxtree file is needed for programs that can deal with taxonomy,
11like Seal and SortByTaxa.
12
13Usage:  taxtree.sh names.dmp nodes.dmp merged.dmp tree.taxtree.gz
14
15Java Parameters:
16-Xmx            This will set Java's memory usage, overriding autodetection.
17                -Xmx20g will specify 20 gigs of RAM.  The max is typically 85% of physical memory.
18-eoom           This flag will cause the process to exit if an out-of-memory
19                exception occurs.  Requires Java 8u92+.
20-da             Disable assertions.
21
22Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
23"
24}
25
26#This block allows symlinked shellscripts to correctly set classpath.
27pushd . > /dev/null
28DIR="${BASH_SOURCE[0]}"
29while [ -h "$DIR" ]; do
30  cd "$(dirname "$DIR")"
31  DIR="$(readlink "$(basename "$DIR")")"
32done
33cd "$(dirname "$DIR")"
34DIR="$(pwd)/"
35popd > /dev/null
36
37#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
38CP="$DIR""current/"
39JNI="-Djava.library.path=""$DIR""jni/"
40JNI=""
41
42z="-Xmx2g"
43z2="-Xms2g"
44set=0
45
46if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
47	usage
48	exit
49fi
50
51calcXmx () {
52	source "$DIR""/calcmem.sh"
53	setEnvironment
54	parseXmx "$@"
55	if [[ $set == 1 ]]; then
56		return
57	fi
58	freeRam 2000m 84
59	z="-Xmx${RAM}m"
60	z2="-Xms${RAM}m"
61}
62calcXmx "$@"
63
64
65taxtree() {
66	local CMD="java $EA $EOOM $z $z2 -cp $CP tax.TaxTree $@"
67	echo $CMD >&2
68	eval $CMD
69}
70
71taxtree "$@"
72