Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/renameimg.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
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| 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 August 23, 2017 | |
| 7 | |
| 8 Description: Renames img records to be prefixed by their id. | |
| 9 This is for internal JGI use and has no external utility. | |
| 10 | |
| 11 Usage: renameimg.sh in=auto out=renamed.fa.gz | |
| 12 | |
| 13 Parameters: | |
| 14 in= 3-column tsv with imgID, taxID, and file path. | |
| 15 These files will have their sequences renamed and concatenated. | |
| 16 img= Optional, if a different (presumably bigger) file will be used for taxonomic assignment. | |
| 17 For example, in could be a subset of img, potentially with incorrect taxIDs. | |
| 18 | |
| 19 Java Parameters: | |
| 20 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 21 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 22 The max is typically 85% of physical memory. | |
| 23 -eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java 8u92+. | |
| 24 -da Disable assertions. | |
| 25 | |
| 26 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 27 " | |
| 28 } | |
| 29 | |
| 30 #This block allows symlinked shellscripts to correctly set classpath. | |
| 31 pushd . > /dev/null | |
| 32 DIR="${BASH_SOURCE[0]}" | |
| 33 while [ -h "$DIR" ]; do | |
| 34 cd "$(dirname "$DIR")" | |
| 35 DIR="$(readlink "$(basename "$DIR")")" | |
| 36 done | |
| 37 cd "$(dirname "$DIR")" | |
| 38 DIR="$(pwd)/" | |
| 39 popd > /dev/null | |
| 40 | |
| 41 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 42 CP="$DIR""current/" | |
| 43 | |
| 44 z="-Xmx1g" | |
| 45 set=0 | |
| 46 | |
| 47 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 48 usage | |
| 49 exit | |
| 50 fi | |
| 51 | |
| 52 calcXmx () { | |
| 53 source "$DIR""/calcmem.sh" | |
| 54 setEnvironment | |
| 55 parseXmx "$@" | |
| 56 } | |
| 57 calcXmx "$@" | |
| 58 | |
| 59 function rename() { | |
| 60 local CMD="java $EA $EOOM $z -cp $CP tax.RenameIMG $@" | |
| 61 echo $CMD >&2 | |
| 62 eval $CMD | |
| 63 } | |
| 64 | |
| 65 rename "$@" |