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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/analyzeaccession.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
6 Last modified September 9, 2019
7
8 Description: Looks at accessions to see how to compress them.
9
10 Usage: analyzeaccession.sh *accession2taxid.gz out=<output file>
11
12 Parameters:
13 perfile=t Use multiple threads per file and multiple files at a time.
14
15 Java Parameters:
16 -Xmx This will set Java's memory usage, overriding autodetection.
17 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
18 specify 200 megs. The max is typically 85% of physical memory.
19 -eoom This flag will cause the process to exit if an out-of-memory
20 exception occurs. Requires Java 8u92+.
21 -da Disable assertions.
22
23 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
24 "
25 }
26
27 #This block allows symlinked shellscripts to correctly set classpath.
28 pushd . > /dev/null
29 DIR="${BASH_SOURCE[0]}"
30 while [ -h "$DIR" ]; do
31 cd "$(dirname "$DIR")"
32 DIR="$(readlink "$(basename "$DIR")")"
33 done
34 cd "$(dirname "$DIR")"
35 DIR="$(pwd)/"
36 popd > /dev/null
37
38 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
39 CP="$DIR""current/"
40
41 z="-Xmx400m"
42 z2="-Xms400m"
43 set=0
44
45 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
46 usage
47 exit
48 fi
49
50 calcXmx () {
51 source "$DIR""/calcmem.sh"
52 setEnvironment
53 parseXmx "$@"
54 }
55 calcXmx "$@"
56
57 a_sample_mt() {
58 local CMD="java $EA $EOOM $z -cp $CP tax.AnalyzeAccession $@"
59 echo $CMD >&2
60 eval $CMD
61 }
62
63 a_sample_mt "$@"