Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/addssu.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified Jan 29, 2020 | |
| 7 | |
| 8 Description: Adds, removes, or replaces SSU sequence of existing sketches. | |
| 9 Sketches and SSU fasta files must be annotated with TaxIDs. | |
| 10 | |
| 11 Usage: addssu.sh in=a.sketch out=b.sketch 16S=16S.fa 18S=18S.fa | |
| 12 | |
| 13 Standard parameters: | |
| 14 in=<file> Input sketch file. | |
| 15 out=<file> Output sketch file. | |
| 16 | |
| 17 Additional files (optional): | |
| 18 16S=<file> A fasta file of 16S sequences. These should be renamed | |
| 19 so that they start with tid|# where # is the taxID. | |
| 20 Should not contain organelle rRNA. | |
| 21 18S=<file> A fasta file of 18S sequences. These should be renamed | |
| 22 so that they start with tid|# where # is the taxID. | |
| 23 Should not contain organelle rRNA. | |
| 24 tree=auto Path to TaxTree, if performing prok/euk-specific operations. | |
| 25 | |
| 26 Processing parameters: | |
| 27 preferSSUMap=f | |
| 28 preferSSUMapEuks=f | |
| 29 preferSSUMapProks=f | |
| 30 SSUMapOnly=f | |
| 31 SSUMapOnlyEuks=f | |
| 32 SSUMapOnlyProks=f | |
| 33 clear16S=f | |
| 34 clear18S=f | |
| 35 clear16SEuks=f | |
| 36 clear18SEuks=f | |
| 37 clear16SProks=f | |
| 38 clear18SProks=f | |
| 39 | |
| 40 | |
| 41 Java Parameters: | |
| 42 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 43 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 44 The max is typically 85% of physical memory. | |
| 45 -da Disable assertions. | |
| 46 | |
| 47 For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt. | |
| 48 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 49 " | |
| 50 } | |
| 51 | |
| 52 #This block allows symlinked shellscripts to correctly set classpath. | |
| 53 pushd . > /dev/null | |
| 54 DIR="${BASH_SOURCE[0]}" | |
| 55 while [ -h "$DIR" ]; do | |
| 56 cd "$(dirname "$DIR")" | |
| 57 DIR="$(readlink "$(basename "$DIR")")" | |
| 58 done | |
| 59 cd "$(dirname "$DIR")" | |
| 60 DIR="$(pwd)/" | |
| 61 popd > /dev/null | |
| 62 | |
| 63 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 64 CP="$DIR""current/" | |
| 65 | |
| 66 z="-Xmx4g" | |
| 67 z2="-Xms4g" | |
| 68 set=0 | |
| 69 | |
| 70 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 71 usage | |
| 72 exit | |
| 73 fi | |
| 74 | |
| 75 calcXmx () { | |
| 76 source "$DIR""/calcmem.sh" | |
| 77 setEnvironment | |
| 78 parseXmx "$@" | |
| 79 if [[ $set == 1 ]]; then | |
| 80 return | |
| 81 fi | |
| 82 #freeRam 3200m 84 | |
| 83 #z="-Xmx${RAM}m" | |
| 84 #z2="-Xms${RAM}m" | |
| 85 } | |
| 86 calcXmx "$@" | |
| 87 | |
| 88 sendsketch() { | |
| 89 local CMD="java $EA $EOOM $z -cp $CP sketch.AddSSU $@" | |
| 90 echo $CMD >&2 | |
| 91 eval $CMD | |
| 92 } | |
| 93 | |
| 94 sendsketch "$@" |