Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/muxbyname.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 June 22, 2016 | |
| 7 | |
| 8 Description: Multiplexes reads from multiple files after renaming them based on their initial file. | |
| 9 Opposite of demuxbyname. | |
| 10 | |
| 11 Usage: muxbyname.sh in=<file,file,file...> out=<output file> | |
| 12 Input files may also be given without an in= prefix, so that you can use wildcards: | |
| 13 muxbyname.sh *.fastq out=muxed.fastq | |
| 14 | |
| 15 | |
| 16 Standard parameters: | |
| 17 in=<file,file> A list of input files. | |
| 18 in2=<file,file> Read 2 input if reads are in paired files. | |
| 19 out=<file> Primary output, or read 1 output. | |
| 20 out2=<file> Read 2 output if reads are in paired files. | |
| 21 overwrite=f (ow) Set to false to force the program to abort rather than | |
| 22 overwrite an existing file. | |
| 23 showspeed=t (ss) Set to 'f' to suppress display of processing speed. | |
| 24 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression | |
| 25 level; lower compression is faster. | |
| 26 | |
| 27 Processing parameters: | |
| 28 None yet! | |
| 29 | |
| 30 Java Parameters: | |
| 31 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 32 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will | |
| 33 specify 200 megs. The max is typically 85% of physical memory. | |
| 34 -eoom This flag will cause the process to exit if an out-of-memory | |
| 35 exception occurs. Requires Java 8u92+. | |
| 36 -da Disable assertions. | |
| 37 | |
| 38 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 39 " | |
| 40 } | |
| 41 | |
| 42 #This block allows symlinked shellscripts to correctly set classpath. | |
| 43 pushd . > /dev/null | |
| 44 DIR="${BASH_SOURCE[0]}" | |
| 45 while [ -h "$DIR" ]; do | |
| 46 cd "$(dirname "$DIR")" | |
| 47 DIR="$(readlink "$(basename "$DIR")")" | |
| 48 done | |
| 49 cd "$(dirname "$DIR")" | |
| 50 DIR="$(pwd)/" | |
| 51 popd > /dev/null | |
| 52 | |
| 53 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 54 CP="$DIR""current/" | |
| 55 | |
| 56 z="-Xmx400m" | |
| 57 z2="-Xms400m" | |
| 58 set=0 | |
| 59 | |
| 60 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 61 usage | |
| 62 exit | |
| 63 fi | |
| 64 | |
| 65 calcXmx () { | |
| 66 source "$DIR""/calcmem.sh" | |
| 67 setEnvironment | |
| 68 parseXmx "$@" | |
| 69 } | |
| 70 calcXmx "$@" | |
| 71 | |
| 72 muxbyname() { | |
| 73 local CMD="java $EA $EOOM $z -cp $CP driver.RenameAndMux $@" | |
| 74 echo $CMD >&2 | |
| 75 eval $CMD | |
| 76 } | |
| 77 | |
| 78 muxbyname "$@" |