Mercurial > repos > rliterman > csp2
comparison 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 |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 #See bbmap.sh for documentation. | |
| 3 | |
| 4 usage(){ | |
| 5 bash "$DIR"bbmap.sh | |
| 6 } | |
| 7 | |
| 8 #This block allows symlinked shellscripts to correctly set classpath. | |
| 9 pushd . > /dev/null | |
| 10 DIR="${BASH_SOURCE[0]}" | |
| 11 while [ -h "$DIR" ]; do | |
| 12 cd "$(dirname "$DIR")" | |
| 13 DIR="$(readlink "$(basename "$DIR")")" | |
| 14 done | |
| 15 cd "$(dirname "$DIR")" | |
| 16 DIR="$(pwd)/" | |
| 17 popd > /dev/null | |
| 18 | |
| 19 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 20 CP="$DIR""current/" | |
| 21 JNI="-Djava.library.path=""$DIR""jni/" | |
| 22 JNI="" | |
| 23 | |
| 24 z="-Xmx1g" | |
| 25 z2="-Xms1g" | |
| 26 set=0 | |
| 27 | |
| 28 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 29 usage | |
| 30 exit | |
| 31 fi | |
| 32 | |
| 33 calcXmx () { | |
| 34 source "$DIR""/calcmem.sh" | |
| 35 setEnvironment | |
| 36 parseXmx "$@" | |
| 37 if [[ $set == 1 ]]; then | |
| 38 return | |
| 39 fi | |
| 40 freeRam 3200m 84 | |
| 41 z="-Xmx${RAM}m" | |
| 42 z2="-Xms${RAM}m" | |
| 43 } | |
| 44 calcXmx "$@" | |
| 45 | |
| 46 mapPacBio() { | |
| 47 if [[ $SHIFTER_RUNTIME == 1 ]]; then | |
| 48 #Ignore NERSC_HOST | |
| 49 shifter=1 | |
| 50 elif [[ $NERSC_HOST == genepool ]]; then | |
| 51 module unload oracle-jdk | |
| 52 module load oracle-jdk/1.8_144_64bit | |
| 53 module load samtools/1.4 | |
| 54 module load pigz | |
| 55 elif [[ $NERSC_HOST == denovo ]]; then | |
| 56 module unload java | |
| 57 module load java/1.8.0_144 | |
| 58 module load PrgEnv-gnu/7.1 | |
| 59 module load samtools/1.4 | |
| 60 module load pigz | |
| 61 elif [[ $NERSC_HOST == cori ]]; then | |
| 62 module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi | |
| 63 module use /global/common/software/m342/nersc-builds/denovo/Modules/usg | |
| 64 module unload java | |
| 65 module load java/1.8.0_144 | |
| 66 module unload PrgEnv-intel | |
| 67 module load PrgEnv-gnu/7.1 | |
| 68 module load samtools/1.4 | |
| 69 module load pigz | |
| 70 fi | |
| 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 $@" | |
| 72 echo $CMD >&2 | |
| 73 eval $CMD | |
| 74 } | |
| 75 | |
| 76 mapPacBio "$@" |