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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbmerge-auto.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 bbmerge-auto.sh is a wrapper for BBMerge that attempts to use all available
6 memory, instead of a fixed amount. This is for use with the Tadpole options
7 of error-correction (ecct) and extension, which require more memory.
8 For merging by overlap only, please use bbmerge.sh. If you set memory
9 manually with the -Xmx flag, bbmerge.sh and bbmerge-auto.sh are equivalent.
10
11 For information about usage and parameters, please run bbmerge.sh.
12 "
13 }
14
15 #This block allows symlinked shellscripts to correctly set classpath.
16 pushd . > /dev/null
17 DIR="${BASH_SOURCE[0]}"
18 while [ -h "$DIR" ]; do
19 cd "$(dirname "$DIR")"
20 DIR="$(readlink "$(basename "$DIR")")"
21 done
22 cd "$(dirname "$DIR")"
23 DIR="$(pwd)/"
24 popd > /dev/null
25
26 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
27 CP="$DIR""current/"
28 JNI="-Djava.library.path=""$DIR""jni/"
29 JNI=""
30
31 z="-Xmx14g"
32 z2="-Xms14g"
33 set=0
34
35 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
36 usage
37 exit
38 fi
39
40 calcXmx () {
41 source "$DIR""/calcmem.sh"
42 setEnvironment
43 parseXmx "$@"
44 if [[ $set == 1 ]]; then
45 return
46 fi
47 freeRam 15000m 84
48 z="-Xmx${RAM}m"
49 z2="-Xms${RAM}m"
50 }
51 calcXmx "$@"
52
53 function merge() {
54 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBMerge $@"
55 echo $CMD >&2
56 eval $CMD
57 }
58
59 merge "$@"