Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbmapskimmer.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 #This is a version of BBMap designed to final all sites above a given threshold, | |
| 4 #rather than the single best site. Syntax is the same as BBMap. | |
| 5 | |
| 6 usage(){ | |
| 7 bash "$DIR"bbmap.sh | |
| 8 } | |
| 9 | |
| 10 #This block allows symlinked shellscripts to correctly set classpath. | |
| 11 pushd . > /dev/null | |
| 12 DIR="${BASH_SOURCE[0]}" | |
| 13 while [ -h "$DIR" ]; do | |
| 14 cd "$(dirname "$DIR")" | |
| 15 DIR="$(readlink "$(basename "$DIR")")" | |
| 16 done | |
| 17 cd "$(dirname "$DIR")" | |
| 18 DIR="$(pwd)/" | |
| 19 popd > /dev/null | |
| 20 | |
| 21 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 22 CP="$DIR""current/" | |
| 23 JNI="-Djava.library.path=""$DIR""jni/" | |
| 24 JNI="" | |
| 25 | |
| 26 z="-Xmx1g" | |
| 27 z2="-Xms1g" | |
| 28 set=0 | |
| 29 | |
| 30 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 31 usage | |
| 32 exit | |
| 33 fi | |
| 34 | |
| 35 calcXmx () { | |
| 36 source "$DIR""/calcmem.sh" | |
| 37 setEnvironment | |
| 38 parseXmx "$@" | |
| 39 if [[ $set == 1 ]]; then | |
| 40 return | |
| 41 fi | |
| 42 freeRam 3200m 84 | |
| 43 z="-Xmx${RAM}m" | |
| 44 z2="-Xms${RAM}m" | |
| 45 } | |
| 46 calcXmx "$@" | |
| 47 | |
| 48 mapPacBioSkimmer() { | |
| 49 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBMapPacBioSkimmer build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambig=all minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@" | |
| 50 echo $CMD >&2 | |
| 51 eval $CMD | |
| 52 } | |
| 53 | |
| 54 mapPacBioSkimmer "$@" |