Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/khist.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 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Description: Generates a histogram of kmer counts for the input reads or assemblies. |
| jpayne@69 | 6 |
| jpayne@69 | 7 Usage: khist.sh in=<input> hist=<histogram output> |
| jpayne@69 | 8 |
| jpayne@69 | 9 Please see bbnorm.sh for more information. |
| jpayne@69 | 10 All the flags are the same, only the parameters (near the bottom of this file) differ. |
| jpayne@69 | 11 " |
| jpayne@69 | 12 } |
| jpayne@69 | 13 |
| jpayne@69 | 14 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 15 pushd . > /dev/null |
| jpayne@69 | 16 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 17 while [ -h "$DIR" ]; do |
| jpayne@69 | 18 cd "$(dirname "$DIR")" |
| jpayne@69 | 19 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 20 done |
| jpayne@69 | 21 cd "$(dirname "$DIR")" |
| jpayne@69 | 22 DIR="$(pwd)/" |
| jpayne@69 | 23 popd > /dev/null |
| jpayne@69 | 24 |
| jpayne@69 | 25 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 26 CP="$DIR""current/" |
| jpayne@69 | 27 |
| jpayne@69 | 28 z="-Xmx31g" |
| jpayne@69 | 29 z2="-Xms31g" |
| jpayne@69 | 30 set=0 |
| jpayne@69 | 31 |
| jpayne@69 | 32 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 33 usage |
| jpayne@69 | 34 exit |
| jpayne@69 | 35 fi |
| jpayne@69 | 36 |
| jpayne@69 | 37 calcXmx () { |
| jpayne@69 | 38 source "$DIR""/calcmem.sh" |
| jpayne@69 | 39 setEnvironment |
| jpayne@69 | 40 parseXmx "$@" |
| jpayne@69 | 41 if [[ $set == 1 ]]; then |
| jpayne@69 | 42 return |
| jpayne@69 | 43 fi |
| jpayne@69 | 44 freeRam 31000m 84 |
| jpayne@69 | 45 z="-Xmx${RAM}m" |
| jpayne@69 | 46 z2="-Xms${RAM}m" |
| jpayne@69 | 47 } |
| jpayne@69 | 48 calcXmx "$@" |
| jpayne@69 | 49 |
| jpayne@69 | 50 khist() { |
| jpayne@69 | 51 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.KmerNormalize bits=32 ecc=f passes=1 keepall dr=f prefilter hist=stdout minprob=0 minqual=0 mindepth=0 minkmers=1 hashes=3 $@" |
| jpayne@69 | 52 echo $CMD >&2 |
| jpayne@69 | 53 eval $CMD |
| jpayne@69 | 54 } |
| jpayne@69 | 55 |
| jpayne@69 | 56 khist "$@" |