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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/taxserver.sh @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell and Shijie Yao
6 Last modified Jan 7, 2020
7
8 Description: Starts a server that translates NCBI taxonomy.
9
10 Usage: taxserver.sh tree=<taxtree file> table=<gitable file> port=<number>
11
12 Usage examples:
13 taxserver.sh tree=tree.taxtree.gz table=gitable.int1d.gz port=1234
14
15 On Genepool:
16 taxserver.sh tree=auto table=auto port=1234
17
18 For accession number support, add accession=<something> E.g.:
19
20 External:
21 taxserver.sh -Xmx45g tree=tree.taxtree.gz table=gitable.int1d.gz accession=prot.accession2taxid.gz,nucl_wgs.accession2taxid.gz port=1234
22
23 On Genepool:
24 taxserver.sh tree=auto table=auto accession=auto port=1234
25
26 If all expected files are in some specific location, you can also do this:
27 taxserver.sh -Xmx45g tree=auto table=auto accession=auto port=1234 taxpath=/path/to/files
28
29 To kill remotely, launch with the flag kill=password, then access /kill/password
30
31 Parameters:
32
33 tree=auto taxtree path. Always necessary.
34 table=auto gitable path. Necessary for gi number support.
35 accession=null Comma-delimited paths of accession files.
36 Necessary for accession support.
37 img=null IMG dump file.
38 pattern=null Pattern file, for storing accessions more efficiently.
39 port=3068 Port number.
40 domain= Domain to be displayed in the help message.
41 Default is taxonomy.jgi-psf.org.
42 dbname= Set the name of the database in the help message.
43 sketchcomparethreads=16 Limit compare threads per connection.
44 sketchloadthreads=4 Limit load threads (for local queries of fastq).
45 sketchonly=f Don't hash taxa names.
46 k=31 Kmer length, 1-32. To maximize sensitivity and
47 specificity, dual kmer lengths may be used: k=31,24
48 prealloc=f Preallocate some data structures for faster loading.
49
50 Security parameters:
51
52 killcode= Set a password to allow remote killing.
53 oldcode= Set the password of a prior instance.
54 oldaddress= Attempt to kill a prior instance after initialization,
55 by sending the old code to this address. For example,
56 taxonomy.jgi-psf.org/kill/
57 allowremotefileaccess=f Allow non-internal queries to use internal files
58 for sketching in local mode.
59 allowlocalhost=f Consider a query internal if it originates from localhost
60 without being proxied.
61 addressprefix=128. Queries originating from this IP address prefix will be
62 considered internal.
63
64
65 Unrecognized parameters with no = symbol will be treated as sketch files.
66 Other sketch parameters such as index and k are also allowed.
67 Please consult bbmap/docs/guides/TaxonomyGuide.txt and BBSketchGuide.txt for more information.
68
69 Java Parameters:
70 -Xmx This will set Java's memory usage, overriding autodetection.
71 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
72 The max is typically 85% of physical memory.
73 -eoom This flag will cause the process to exit if an
74 out-of-memory exception occurs. Requires Java 8u92+.
75 -da Disable assertions.
76
77 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
78 "
79 }
80
81 #This block allows symlinked shellscripts to correctly set classpath.
82 pushd . > /dev/null
83 DIR="${BASH_SOURCE[0]}"
84 while [ -h "$DIR" ]; do
85 cd "$(dirname "$DIR")"
86 DIR="$(readlink "$(basename "$DIR")")"
87 done
88 cd "$(dirname "$DIR")"
89 DIR="$(pwd)/"
90 popd > /dev/null
91
92 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
93 CP="$DIR""current/"
94
95 z="-Xmx45g"
96 z2="-Xms45g"
97 set=0
98
99 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
100 usage
101 exit
102 fi
103
104 calcXmx () {
105 source "$DIR""/calcmem.sh"
106 setEnvironment
107 parseXmx "$@"
108 }
109 calcXmx "$@"
110
111 taxserver() {
112 local CMD="java $EA $EOOM $z $z2 -cp $CP tax.TaxServer $@"
113 echo $CMD >&2
114 eval $CMD
115 }
116
117 taxserver "$@"