Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mapPacBio.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 #See bbmap.sh for documentation. |
| jpayne@69 | 3 |
| jpayne@69 | 4 usage(){ |
| jpayne@69 | 5 bash "$DIR"bbmap.sh |
| jpayne@69 | 6 } |
| jpayne@69 | 7 |
| jpayne@69 | 8 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 9 pushd . > /dev/null |
| jpayne@69 | 10 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 11 while [ -h "$DIR" ]; do |
| jpayne@69 | 12 cd "$(dirname "$DIR")" |
| jpayne@69 | 13 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 14 done |
| jpayne@69 | 15 cd "$(dirname "$DIR")" |
| jpayne@69 | 16 DIR="$(pwd)/" |
| jpayne@69 | 17 popd > /dev/null |
| jpayne@69 | 18 |
| jpayne@69 | 19 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 20 CP="$DIR""current/" |
| jpayne@69 | 21 JNI="-Djava.library.path=""$DIR""jni/" |
| jpayne@69 | 22 JNI="" |
| jpayne@69 | 23 |
| jpayne@69 | 24 z="-Xmx1g" |
| jpayne@69 | 25 z2="-Xms1g" |
| jpayne@69 | 26 set=0 |
| jpayne@69 | 27 |
| jpayne@69 | 28 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 29 usage |
| jpayne@69 | 30 exit |
| jpayne@69 | 31 fi |
| jpayne@69 | 32 |
| jpayne@69 | 33 calcXmx () { |
| jpayne@69 | 34 source "$DIR""/calcmem.sh" |
| jpayne@69 | 35 setEnvironment |
| jpayne@69 | 36 parseXmx "$@" |
| jpayne@69 | 37 if [[ $set == 1 ]]; then |
| jpayne@69 | 38 return |
| jpayne@69 | 39 fi |
| jpayne@69 | 40 freeRam 3200m 84 |
| jpayne@69 | 41 z="-Xmx${RAM}m" |
| jpayne@69 | 42 z2="-Xms${RAM}m" |
| jpayne@69 | 43 } |
| jpayne@69 | 44 calcXmx "$@" |
| jpayne@69 | 45 |
| jpayne@69 | 46 mapPacBio() { |
| jpayne@69 | 47 if [[ $SHIFTER_RUNTIME == 1 ]]; then |
| jpayne@69 | 48 #Ignore NERSC_HOST |
| jpayne@69 | 49 shifter=1 |
| jpayne@69 | 50 elif [[ $NERSC_HOST == genepool ]]; then |
| jpayne@69 | 51 module unload oracle-jdk |
| jpayne@69 | 52 module load oracle-jdk/1.8_144_64bit |
| jpayne@69 | 53 module load samtools/1.4 |
| jpayne@69 | 54 module load pigz |
| jpayne@69 | 55 elif [[ $NERSC_HOST == denovo ]]; then |
| jpayne@69 | 56 module unload java |
| jpayne@69 | 57 module load java/1.8.0_144 |
| jpayne@69 | 58 module load PrgEnv-gnu/7.1 |
| jpayne@69 | 59 module load samtools/1.4 |
| jpayne@69 | 60 module load pigz |
| jpayne@69 | 61 elif [[ $NERSC_HOST == cori ]]; then |
| jpayne@69 | 62 module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi |
| jpayne@69 | 63 module use /global/common/software/m342/nersc-builds/denovo/Modules/usg |
| jpayne@69 | 64 module unload java |
| jpayne@69 | 65 module load java/1.8.0_144 |
| jpayne@69 | 66 module unload PrgEnv-intel |
| jpayne@69 | 67 module load PrgEnv-gnu/7.1 |
| jpayne@69 | 68 module load samtools/1.4 |
| jpayne@69 | 69 module load pigz |
| jpayne@69 | 70 fi |
| jpayne@69 | 71 local CMD="java $EA $EOOM $z -cp $CP align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 $@" |
| jpayne@69 | 72 echo $CMD >&2 |
| jpayne@69 | 73 eval $CMD |
| jpayne@69 | 74 } |
| jpayne@69 | 75 |
| jpayne@69 | 76 mapPacBio "$@" |