changeset 0:88a8e2392731 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makeTSSdist_wrapper_hist.sh	Mon Jan 04 10:21:43 2016 -0500
@@ -0,0 +1,81 @@
+#!/bin/bash
+
+REG="NA"
+CONTROLFILE="NA"
+
+while getopts "f:c:l:o:r:u:v:e:p:" optionName; do
+case "$optionName" in
+
+f) CHIPFILE="$OPTARG";;
+c) CONTROLFILE="$OPTARG";;
+l) STEP="$OPTARG";;
+r) RIGHT="$OPTARG";;
+o) OUTPUT="$OPTARG";;
+u) OUTSTAT="$OPTARG";;
+v) GENOME="$OPTARG";;
+e) REG="$OPTARG";;
+p) PDF="$OPTARG";;
+
+esac
+done
+
+LOGTMP=$OUTPUT.log.tmp
+
+#LOGTMP=/data/tmp/log.tmp
+
+#echo $LOGTMP
+#echo "$@"
+
+echo "$@" >> $LOGTMP
+
+LOCAL_DIR=`( cd -P $(dirname $0); pwd)`
+DOCKER_PATH='/usr/bin/maketssdist_histones'
+
+
+OUTPUT_DIR=`dirname $OUTPUT`
+R_PATH='/usr/bin/R-3.1.0/bin/Rscript --slave '
+
+databasePath=$(find / -type d -name files | grep database)
+
+mkdir -p $databasePath/nebulaAnnotations
+mkdir -p $databasePath/nebulaAnnotations/noIdenticalTransc
+nebulaAnnotationPath=$databasePath/nebulaAnnotations
+[ ! -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/$GENOME.noIdenticalTransc.txt
+
+noIdenticalTranscPath=$nebulaAnnotationPath/noIdenticalTransc
+
+if [ -r $REG ]; then
+  echo "1:  perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -reg $REG -o $OUTPUT.annotated" >> $LOGTMP
+  perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -reg $REG -o $OUTPUT.annotated >> $LOGTMP 2>> $LOGTMP
+ else
+  echo "2:  perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -reg $REG -o $OUTPUT.annotated" >> $LOGTMP
+  perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f $CHIPFILE -o $OUTPUT.annotated >> $LOGTMP 2>> $LOGTMP
+fi
+
+if [ -r $CONTROLFILE ]; then
+  #create a subset of control peaks (highest peaks, the same number as in the sample) 
+   echo "   perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o ${OUTPUT_DIR}/control.tmp" >>$LOGTMP
+   perl $DOCKER_PATH/createControlPeakSubSet.pl -f $CHIPFILE -c $CONTROLFILE -o ${OUTPUT_DIR}/control.tmp >>$LOGTMP 2>>$LOGTMP
+  if [ -r $REG ]; then
+    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
+  else
+    perl $DOCKER_PATH/crossBedWithGenes_hist.pl -g $noIdenticalTranscPath/$GENOME.noIdenticalTransc.txt -f ${OUTPUT_DIR}/control.tmp -o $OUTPUT.control.annotated >> $LOGTMP 2>> $LOGTMP
+  fi
+  echo "3: cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $OUTPUT.control.annotated $PDF" >> $LOGTMP
+  cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $OUTPUT.control.annotated $PDF >>$LOGTMP 2>>$LOGTMP
+else
+  echo "4:  cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $PDF 2>>$LOGTMP" >>$LOGTMP
+  cat $DOCKER_PATH/makeTSSdist_hist.R | R --slave --args $STEP $RIGHT $OUTPUT.annotated $OUTPUT $OUTSTAT $PDF 2>>$LOGTMP >>$LOGTMP
+fi
+
+if [ -r $LOGTMP ]; then
+  rm $LOGTMP
+fi
+
+rm $OUTPUT.annotated*
+
+if [ -r $CONTROLFILE ]; then
+  rm $OUTPUT.control.annotated*
+  rm ${OUTPUT_DIR}/control.tmp
+fi
+