Mercurial > repos > rliterman > csp2
annotate 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 |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 #This is a version of BBMap designed to final all sites above a given threshold, |
| jpayne@69 | 4 #rather than the single best site. Syntax is the same as BBMap. |
| jpayne@69 | 5 |
| jpayne@69 | 6 usage(){ |
| jpayne@69 | 7 bash "$DIR"bbmap.sh |
| jpayne@69 | 8 } |
| jpayne@69 | 9 |
| jpayne@69 | 10 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 11 pushd . > /dev/null |
| jpayne@69 | 12 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 13 while [ -h "$DIR" ]; do |
| jpayne@69 | 14 cd "$(dirname "$DIR")" |
| jpayne@69 | 15 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 16 done |
| jpayne@69 | 17 cd "$(dirname "$DIR")" |
| jpayne@69 | 18 DIR="$(pwd)/" |
| jpayne@69 | 19 popd > /dev/null |
| jpayne@69 | 20 |
| jpayne@69 | 21 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 22 CP="$DIR""current/" |
| jpayne@69 | 23 JNI="-Djava.library.path=""$DIR""jni/" |
| jpayne@69 | 24 JNI="" |
| jpayne@69 | 25 |
| jpayne@69 | 26 z="-Xmx1g" |
| jpayne@69 | 27 z2="-Xms1g" |
| jpayne@69 | 28 set=0 |
| jpayne@69 | 29 |
| jpayne@69 | 30 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 31 usage |
| jpayne@69 | 32 exit |
| jpayne@69 | 33 fi |
| jpayne@69 | 34 |
| jpayne@69 | 35 calcXmx () { |
| jpayne@69 | 36 source "$DIR""/calcmem.sh" |
| jpayne@69 | 37 setEnvironment |
| jpayne@69 | 38 parseXmx "$@" |
| jpayne@69 | 39 if [[ $set == 1 ]]; then |
| jpayne@69 | 40 return |
| jpayne@69 | 41 fi |
| jpayne@69 | 42 freeRam 3200m 84 |
| jpayne@69 | 43 z="-Xmx${RAM}m" |
| jpayne@69 | 44 z2="-Xms${RAM}m" |
| jpayne@69 | 45 } |
| jpayne@69 | 46 calcXmx "$@" |
| jpayne@69 | 47 |
| jpayne@69 | 48 mapPacBioSkimmer() { |
| jpayne@69 | 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 $@" |
| jpayne@69 | 50 echo $CMD >&2 |
| jpayne@69 | 51 eval $CMD |
| jpayne@69 | 52 } |
| jpayne@69 | 53 |
| jpayne@69 | 54 mapPacBioSkimmer "$@" |