Mercurial > repos > jbrayet > annotategenes_histones_1_0_docker
comparison annotateGenes_hist_wrapper.sh @ 6:94be3cc05503 draft default tip
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author | jbrayet |
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date | Tue, 05 Jan 2016 08:16:10 -0500 |
parents | 9947321ac2a0 |
children |
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5:af81818b403c | 6:94be3cc05503 |
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103 noIdenticalTranscPath=$nebulaAnnotationPath/noIdenticalTransc | 103 noIdenticalTranscPath=$nebulaAnnotationPath/noIdenticalTransc |
104 | 104 |
105 echo "ChIP:" >$LOG | 105 echo "ChIP:" >$LOG |
106 | 106 |
107 if [ -r $REG ]; then | 107 if [ -r $REG ]; then |
108 echo "1: perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -selG $REG -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE" >> $LOGTMP | 108 echo "1: perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -selG $REG -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE" >> $LOGTMP |
109 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -selG $REG -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP | 109 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -selG $REG -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP |
110 else | 110 else |
111 echo "2: perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE " >> $LOGTMP | 111 echo "2: perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE " >> $LOGTMP |
112 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP | 112 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -o $OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP |
113 fi | 113 fi |
114 | 114 |
115 | 115 |
116 | 116 |
117 if [ -r $CONTROLFILE ]; then | 117 if [ -r $CONTROLFILE ]; then |
119 echo "Control:" >>$LOG | 119 echo "Control:" >>$LOG |
120 #create a subset of control peaks (highest peaks, the same number as in the sample) | 120 #create a subset of control peaks (highest peaks, the same number as in the sample) |
121 echo " perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o $CONTROLFILE.tmp -n $BOOTSTRAP " >>$LOGTMP | 121 echo " perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o $CONTROLFILE.tmp -n $BOOTSTRAP " >>$LOGTMP |
122 perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o $CONTROLFILE.tmp -n $BOOTSTRAP >>$LOGTMP 2>>$LOGTMP | 122 perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o $CONTROLFILE.tmp -n $BOOTSTRAP >>$LOGTMP 2>>$LOGTMP |
123 if [ -r $REG ]; then | 123 if [ -r $REG ]; then |
124 echo "5: perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp -selG $REG -o $CONTROLSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE ">> $LOGTMP | 124 echo "5: perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp -selG $REG -o $CONTROLSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE ">> $LOGTMP |
125 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp -selG $REG -o $CONTROLSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP | 125 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp -selG $REG -o $CONTROLSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP |
126 for (( i=2; i<=$BOOTSTRAP; i++ )) | 126 for (( i=2; i<=$BOOTSTRAP; i++ )) |
127 do | 127 do |
128 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp$i -selG $REG -o $CONTROLSTAT$i -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP | 128 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp$i -selG $REG -o $CONTROLSTAT$i -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP |
129 done | 129 done |
130 else | 130 else |
131 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp -o $CONTROLSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP | 131 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp -o $CONTROLSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP |
132 for (( i=2; i<=$BOOTSTRAP; i++ )) | 132 for (( i=2; i<=$BOOTSTRAP; i++ )) |
133 do | 133 do |
134 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp$i -o $CONTROLSTAT$i -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP | 134 perl $DOCKER_PATH/geneAnnotation_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -tf $CONTROLFILE.tmp$i -o $CONTROLSTAT$i -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE >>$LOG 2>> $LOGTMP |
135 done | 135 done |
136 | 136 |
137 fi | 137 fi |
138 echo "3: $R_PATH $DOCKER_PATH/geneDist_hist.R | R --slave --args $OUTSTAT $OUTPUT $LOG $CONTROLSTAT $PDF $BOOTSTRAP " >>$LOGTMP | 138 echo "3: $R_PATH $DOCKER_PATH/geneDist_hist.R | R --slave --args $OUTSTAT $OUTPUT $LOG $CONTROLSTAT $PDF $BOOTSTRAP " >>$LOGTMP |
139 $R_PATH $DOCKER_PATH/geneDist_hist.R --args $OUTSTAT $OUTPUT $LOG $CONTROLSTAT $PDF $BOOTSTRAP 2>>$LOGTMP >>$LOGTMP | 139 $R_PATH $DOCKER_PATH/geneDist_hist.R --args $OUTSTAT $OUTPUT $LOG $CONTROLSTAT $PDF $BOOTSTRAP 2>>$LOGTMP >>$LOGTMP |