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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/subsketch.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 Jan 7, 2020
7
8 Description: Shrinks sketches to a smaller fixed length.
9
10 Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
11
12 Usage: subsketch.sh in=file.sketch out=sub.sketch size=1000 autosize=f
13 Bulk usage: subsketch.sh in=big#.sketch out=small#.sketch sizemult=0.5
14
15 Standard parameters:
16 in=<file> Input sketch file containing one or more sketches.
17 out=<file> Output sketch file.
18 size=10000 Size of sketches to generate, if autosize=f.
19 autosize=t Autosize sketches based on genome size.
20 sizemult=1 Adjust default sketch autosize by this factor.
21 blacklist= Apply a blacklist to the sketch before resizing.
22 files=31 If the output filename contains a # symbol,
23 spread the output across this many files, replacing
24 the # with a number.
25
26 Java Parameters:
27 -Xmx This will set Java's memory usage, overriding autodetection.
28 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
29 The max is typically 85% of physical memory.
30 -eoom This flag will cause the process to exit if an out-of-memory
31 exception occurs. Requires Java 8u92+.
32 -da Disable assertions.
33
34 For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
35 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
36 "
37 }
38
39 #This block allows symlinked shellscripts to correctly set classpath.
40 pushd . > /dev/null
41 DIR="${BASH_SOURCE[0]}"
42 while [ -h "$DIR" ]; do
43 cd "$(dirname "$DIR")"
44 DIR="$(readlink "$(basename "$DIR")")"
45 done
46 cd "$(dirname "$DIR")"
47 DIR="$(pwd)/"
48 popd > /dev/null
49
50 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
51 CP="$DIR""current/"
52
53 z="-Xmx4g"
54 z2="-Xms4g"
55 set=0
56
57 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
58 usage
59 exit
60 fi
61
62 calcXmx () {
63 source "$DIR""/calcmem.sh"
64 setEnvironment
65 parseXmx "$@"
66 if [[ $set == 1 ]]; then
67 return
68 fi
69 freeRam 3200m 84
70 z="-Xmx${RAM}m"
71 z2="-Xms${RAM}m"
72 }
73 calcXmx "$@"
74
75 sendsketch() {
76 local CMD="java $EA $EOOM $z -cp $CP sketch.SubSketch $@"
77 # echo $CMD >&2
78 eval $CMD
79 }
80
81 sendsketch "$@"