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1 #!/bin/bash
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2
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3 REG="NA"
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4 CONTROLFILE="NA"
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5
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6 while getopts "f:c:l:o:r:u:v:e:p:" optionName; do
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7 case "$optionName" in
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8
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9 f) CHIPFILE="$OPTARG";;
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10 c) CONTROLFILE="$OPTARG";;
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11 l) STEP="$OPTARG";;
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12 r) RIGHT="$OPTARG";;
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13 o) OUTPUT="$OPTARG";;
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14 u) OUTSTAT="$OPTARG";;
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15 v) GENOME="$OPTARG";;
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16 e) REG="$OPTARG";;
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17 p) PDF="$OPTARG";;
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18
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19 esac
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20 done
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21
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22 LOGTMP=$OUTPUT.log.tmp
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23
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24 #LOGTMP=/data/tmp/log.tmp
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25
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26 #echo $LOGTMP
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27 #echo "$@"
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28
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29 echo "$@" >> $LOGTMP
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30
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31 LOCAL_DIR=`( cd -P $(dirname $0); pwd)`
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32 DOCKER_PATH='/usr/bin/maketssdist_histones'
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33
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34
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35 OUTPUT_DIR=`dirname $OUTPUT`
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6
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36 R_PATH='Rscript --slave '
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0
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37
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38 databasePath=$(find / -type d -name files | grep database)
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39
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40 mkdir -p $databasePath/nebulaAnnotations
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41 mkdir -p $databasePath/nebulaAnnotations/noIdenticalTransc
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42 nebulaAnnotationPath=$databasePath/nebulaAnnotations
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43 [ ! -f $nebulaAnnotationPath/noIdenticalTransc/$GENOME.noIdenticalTransc.txt ] && curl -s -o $nebulaAnnotationPath/noIdenticalTransc/$GENOME.noIdenticalTransc.txt -L https://github.com/jbrayet/nebula_tools_docker/raw/master/tools_data/noIdenticalTransc/$GENOME.noIdenticalTransc.txt
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44
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45 noIdenticalTranscPath=$nebulaAnnotationPath/noIdenticalTransc
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46
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47 if [ -r $REG ]; then
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48 echo "1: perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -reg $REG -o $OUTPUT.annotated" >> $LOGTMP
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49 perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -reg $REG -o $OUTPUT.annotated >> $LOGTMP 2>> $LOGTMP
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50 else
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51 echo "2: perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -reg $REG -o $OUTPUT.annotated" >> $LOGTMP
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52 perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -o $OUTPUT.annotated >> $LOGTMP 2>> $LOGTMP
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53 fi
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54
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55 if [ -r $CONTROLFILE ]; then
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56 #create a subset of control peaks (highest peaks, the same number as in the sample)
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57 echo " perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o ${OUTPUT_DIR}/control.tmp" >>$LOGTMP
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58 perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o ${OUTPUT_DIR}/control.tmp >>$LOGTMP 2>>$LOGTMP
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59 if [ -r $REG ]; then
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60 perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f ${OUTPUT_DIR}/control.tmp -reg $REG -o $OUTPUT.control.annotated >> $LOGTMP 2>> $LOGTMP
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61 else
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62 perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f ${OUTPUT_DIR}/control.tmp -o $OUTPUT.control.annotated >> $LOGTMP 2>> $LOGTMP
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63 fi
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64 echo "3: cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $OUTPUT.control.annotated $PDF" >> $LOGTMP
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65 cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $OUTPUT.control.annotated $PDF >>$LOGTMP 2>>$LOGTMP
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66 else
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67 echo "4: cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $PDF 2>>$LOGTMP" >>$LOGTMP
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68 cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $PDF 2>>$LOGTMP >>$LOGTMP
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69 fi
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70
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71 if [ -r $LOGTMP ]; then
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72 rm $LOGTMP
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73 fi
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74
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75 rm $OUTPUT.annotated*
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76
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77 if [ -r $CONTROLFILE ]; then
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78 rm $OUTPUT.control.annotated*
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79 rm ${OUTPUT_DIR}/control.tmp
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80 fi
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81
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