Mercurial > repos > jbrayet > annotategenes_histones_1_0_docker

comparison annotateGenes_hist_wrapper.sh @ 6:94be3cc05503 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jbrayet
date Tue, 05 Jan 2016 08:16:10 -0500
parents 9947321ac2a0
children
comparison
equal deleted inserted replaced
5:af81818b403c 6:94be3cc05503
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