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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 September 18, 2019
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7
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8 Description: Runs TadpoleWrapper after some preprocessing,
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9 to allow optimal assemblies using long kmers.
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10 Only paired reads are supported.
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11
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12 Usage:
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13 tadpipe.sh in=reads.fq out=contigs.fa
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14
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15
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16 Parameters:
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17 in=<file> Input reads.
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18 in2=<file> Optional read 2, if reads are in two files.
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19 out=contigs.fa Output file name.
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20 temp=$TMPDIR Path to a directory for temp files.
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21 delete=t Delete intermediate files.
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22 gz=f Gzip intermediate files.
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23
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24 Other parameters can be passed to individual phases like this:
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25
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26 assemble_k=200,250 Set kmer lengths for assembly phase.
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27 merge_strict Set the strict flag in merge phase.
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28 extend_el=120 Set the left-extension distance in the extension phase.
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29
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30 Valid prefixes:
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31
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32 filter_ PhiX and contaminant filtering.
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33 trim_ Adapter trimmming.
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34 merge_ Paired-read merging.
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35 correct_ Error correction.
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36 extend_ Read extension.
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37 assemble_ Final assembly.
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38 "
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39 }
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40
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41 #This block allows symlinked shellscripts to correctly set classpath.
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42 pushd . > /dev/null
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43 DIR="${BASH_SOURCE[0]}"
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44 while [ -h "$DIR" ]; do
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45 cd "$(dirname "$DIR")"
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46 DIR="$(readlink "$(basename "$DIR")")"
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47 done
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48 cd "$(dirname "$DIR")"
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49 DIR="$(pwd)/"
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50 popd > /dev/null
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51
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52 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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53 CP="$DIR""current/"
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54
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55 z="-Xmx14g"
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56 z2="-Xms14g"
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57 set=0
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58
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59 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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60 usage
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61 exit
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62 fi
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63
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64 calcXmx () {
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65 source "$DIR""/calcmem.sh"
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66 setEnvironment
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67 parseXmx "$@"
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68 if [[ $set == 1 ]]; then
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69 return
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70 fi
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71 freeRam 15000m 84
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72 z="-Xmx${RAM}m"
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73 z2="-Xms${RAM}m"
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74 }
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75 calcXmx "$@"
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76
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77 tadpipe() {
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78 local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.TadPipe $@"
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79 echo $CMD >&2
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80 eval $CMD
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81 }
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82
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83 tadpipe "$@"
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