Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mergeOTUs.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 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified January 21, 2015 | |
| 7 | |
| 8 Description: Merges coverage stats lines (from pileup) for the same OTU, | |
| 9 according to some custom naming scheme. | |
| 10 | |
| 11 Usage: mergeOTUs.sh in=<file> out=<file> | |
| 12 | |
| 13 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 14 " | |
| 15 } | |
| 16 | |
| 17 #This block allows symlinked shellscripts to correctly set classpath. | |
| 18 pushd . > /dev/null | |
| 19 DIR="${BASH_SOURCE[0]}" | |
| 20 while [ -h "$DIR" ]; do | |
| 21 cd "$(dirname "$DIR")" | |
| 22 DIR="$(readlink "$(basename "$DIR")")" | |
| 23 done | |
| 24 cd "$(dirname "$DIR")" | |
| 25 DIR="$(pwd)/" | |
| 26 popd > /dev/null | |
| 27 | |
| 28 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 29 CP="$DIR""current/" | |
| 30 | |
| 31 z="-Xmx1g" | |
| 32 set=0 | |
| 33 | |
| 34 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 35 usage | |
| 36 exit | |
| 37 fi | |
| 38 | |
| 39 calcXmx () { | |
| 40 source "$DIR""/calcmem.sh" | |
| 41 setEnvironment | |
| 42 parseXmx "$@" | |
| 43 } | |
| 44 calcXmx "$@" | |
| 45 | |
| 46 function mergeOTUs() { | |
| 47 local CMD="java $EA $EOOM $z -cp $CP driver.MergeCoverageOTU $@" | |
| 48 echo $CMD >&2 | |
| 49 eval $CMD | |
| 50 } | |
| 51 | |
| 52 mergeOTUs "$@" |