Mercurial > repos > rliterman > csp2
annotate 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 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Written by Brian Bushnell |
| jpayne@69 | 6 Last modified August 23, 2017 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Description: Renames img records to be prefixed by their id. |
| jpayne@69 | 9 This is for internal JGI use and has no external utility. |
| jpayne@69 | 10 |
| jpayne@69 | 11 Usage: renameimg.sh in=auto out=renamed.fa.gz |
| jpayne@69 | 12 |
| jpayne@69 | 13 Parameters: |
| jpayne@69 | 14 in= 3-column tsv with imgID, taxID, and file path. |
| jpayne@69 | 15 These files will have their sequences renamed and concatenated. |
| jpayne@69 | 16 img= Optional, if a different (presumably bigger) file will be used for taxonomic assignment. |
| jpayne@69 | 17 For example, in could be a subset of img, potentially with incorrect taxIDs. |
| jpayne@69 | 18 |
| jpayne@69 | 19 Java Parameters: |
| jpayne@69 | 20 -Xmx This will set Java's memory usage, overriding autodetection. |
| jpayne@69 | 21 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. |
| jpayne@69 | 22 The max is typically 85% of physical memory. |
| jpayne@69 | 23 -eoom This flag will cause the process to exit if an out-of-memory exception occurs. Requires Java 8u92+. |
| jpayne@69 | 24 -da Disable assertions. |
| jpayne@69 | 25 |
| jpayne@69 | 26 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. |
| jpayne@69 | 27 " |
| jpayne@69 | 28 } |
| jpayne@69 | 29 |
| jpayne@69 | 30 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 31 pushd . > /dev/null |
| jpayne@69 | 32 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 33 while [ -h "$DIR" ]; do |
| jpayne@69 | 34 cd "$(dirname "$DIR")" |
| jpayne@69 | 35 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 36 done |
| jpayne@69 | 37 cd "$(dirname "$DIR")" |
| jpayne@69 | 38 DIR="$(pwd)/" |
| jpayne@69 | 39 popd > /dev/null |
| jpayne@69 | 40 |
| jpayne@69 | 41 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 42 CP="$DIR""current/" |
| jpayne@69 | 43 |
| jpayne@69 | 44 z="-Xmx1g" |
| jpayne@69 | 45 set=0 |
| jpayne@69 | 46 |
| jpayne@69 | 47 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 48 usage |
| jpayne@69 | 49 exit |
| jpayne@69 | 50 fi |
| jpayne@69 | 51 |
| jpayne@69 | 52 calcXmx () { |
| jpayne@69 | 53 source "$DIR""/calcmem.sh" |
| jpayne@69 | 54 setEnvironment |
| jpayne@69 | 55 parseXmx "$@" |
| jpayne@69 | 56 } |
| jpayne@69 | 57 calcXmx "$@" |
| jpayne@69 | 58 |
| jpayne@69 | 59 function rename() { |
| jpayne@69 | 60 local CMD="java $EA $EOOM $z -cp $CP tax.RenameIMG $@" |
| jpayne@69 | 61 echo $CMD >&2 |
| jpayne@69 | 62 eval $CMD |
| jpayne@69 | 63 } |
| jpayne@69 | 64 |
| jpayne@69 | 65 rename "$@" |