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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell
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6 Last modified March 19, 2018
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7
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8 Description: Summarizes monthly contam files into a single file.
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9 This is for internal JGI use.
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10
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11 Usage: summarizecontam.sh <input files> out=<output file>
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12
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13 Parameters:
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14 in=<file,file> Input contam summary files, comma-delimited.
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15 Alternately, file arguments (from a * expansion) will be
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16 considered input files.
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17 out=<file> Output.
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18 tree=auto Taxtree file location (optional).
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19 overwrite=t (ow) Set to false to force the program to abort rather than
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20 overwrite an existing file.
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21
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22 Filter Parameters (passing all required to pass):
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23 minreads=0 Ignore records with fewer reads than this.
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24 minsequnits=0 Ignore records with fewer seq units than this.
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25
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26 Java Parameters:
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27 -Xmx This will set Java's memory usage, overriding autodetection.
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28 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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29 specify 200 megs. The max is typically 85% of physical memory.
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30 -eoom This flag will cause the process to exit if an out-of-memory
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31 exception occurs. Requires Java 8u92+.
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32 -da Disable assertions.
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33
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34 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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35 "
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36 }
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37
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38 #This block allows symlinked shellscripts to correctly set classpath.
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39 pushd . > /dev/null
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40 DIR="${BASH_SOURCE[0]}"
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41 while [ -h "$DIR" ]; do
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42 cd "$(dirname "$DIR")"
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43 DIR="$(readlink "$(basename "$DIR")")"
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44 done
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45 cd "$(dirname "$DIR")"
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46 DIR="$(pwd)/"
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47 popd > /dev/null
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48
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49 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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50 CP="$DIR""current/"
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51
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52 z="-Xmx1g"
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53 z2="-Xms1g"
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54 set=0
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55
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56 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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57 usage
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58 exit
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59 fi
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60
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61 calcXmx () {
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62 source "$DIR""/calcmem.sh"
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63 setEnvironment
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64 parseXmx "$@"
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65 if [[ $set == 1 ]]; then
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66 return
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67 fi
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68 freeRam 1000m 24
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69 z="-Xmx${RAM}m"
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70 z2="-Xms${RAM}m"
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71 }
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72 calcXmx "$@"
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73
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74 process() {
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75 local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeContamReport $@"
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76 echo $CMD >&2
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77 eval $CMD
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78 }
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79
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80 process "$@"
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