Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbwrap.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 Last modified February 13, 2020 | |
| 6 | |
| 7 Description: Wrapper for BBMap to allow multiple input and output files for the same reference. | |
| 8 | |
| 9 To index: bbwrap.sh ref=<reference fasta> | |
| 10 To map: bbwrap.sh in=<file,file,...> out=<file,file,...> | |
| 11 To map without an index: bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk | |
| 12 To map pairs and singletons and output them into the same file: | |
| 13 bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append | |
| 14 | |
| 15 BBWrap will not work with stdin and stdout, or histogram output. | |
| 16 | |
| 17 Other Parameters: | |
| 18 | |
| 19 in=<file,file> Input sequences to map. | |
| 20 inlist=<fofn> Alternately, input and output can be a file of filenames, | |
| 21 one line per file, using the flag inlist, outlist, outmlist, | |
| 22 in2list, etc. | |
| 23 mapper=bbmap Select mapper. May be BBMap, BBMapPacBio, | |
| 24 or BBMapPacBioSkimmer. | |
| 25 append=f Append to files rather than overwriting them. | |
| 26 If append is enabled, and there is exactly one output file, | |
| 27 all output will be written to that file. | |
| 28 | |
| 29 ***** All BBMap parameters can be used; see bbmap.sh for more details. ***** | |
| 30 " | |
| 31 } | |
| 32 | |
| 33 #This block allows symlinked shellscripts to correctly set classpath. | |
| 34 pushd . > /dev/null | |
| 35 DIR="${BASH_SOURCE[0]}" | |
| 36 while [ -h "$DIR" ]; do | |
| 37 cd "$(dirname "$DIR")" | |
| 38 DIR="$(readlink "$(basename "$DIR")")" | |
| 39 done | |
| 40 cd "$(dirname "$DIR")" | |
| 41 DIR="$(pwd)/" | |
| 42 popd > /dev/null | |
| 43 | |
| 44 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 45 CP="$DIR""current/" | |
| 46 JNI="-Djava.library.path=""$DIR""jni/" | |
| 47 JNI="" | |
| 48 | |
| 49 z="-Xmx1g" | |
| 50 z2="-Xms1g" | |
| 51 set=0 | |
| 52 | |
| 53 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 54 usage | |
| 55 exit | |
| 56 fi | |
| 57 | |
| 58 calcXmx () { | |
| 59 source "$DIR""/calcmem.sh" | |
| 60 setEnvironment | |
| 61 parseXmx "$@" | |
| 62 if [[ $set == 1 ]]; then | |
| 63 return | |
| 64 fi | |
| 65 freeRam 3200m 84 | |
| 66 z="-Xmx${RAM}m" | |
| 67 z2="-Xms${RAM}m" | |
| 68 } | |
| 69 calcXmx "$@" | |
| 70 | |
| 71 bbwrap() { | |
| 72 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@" | |
| 73 echo $CMD >&2 | |
| 74 eval $CMD | |
| 75 } | |
| 76 | |
| 77 bbwrap "$@" |