fix: attempt to obviate need for absolute paths

CCBR · Jan 22, 2025 · ea99c0c · ea99c0c
1 parent b4613b0
commit ea99c0c
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Showing 3 changed files with 32 additions and 36 deletions.
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -13,7 +13,7 @@ env:
   IMAGE_NAME: recap
   CONTEXT: "./"
   NAMESPACE: nciccbr
-  VERSION_TAG: 0.3.1
+  VERSION_TAG: 0.3.2
 
 jobs:
   build-docker:

diff --git a/RECAP_MACS.sh b/RECAP_MACS.sh
@@ -32,11 +32,7 @@
 
 # ===============================================================
 # Script version number
-VERSION="1.0.2"     
-# Provide a variable for the location of this and other scripts
-SCRIPT_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-REMIX_PATH=RECAP_Re-Mix.sh
-PERL_PATH=RECAP.pl
+VERSION="1.0.2"
 # Text display commands
 bold=$(tput bold)
 normal=$(tput sgr0)
@@ -62,8 +58,6 @@ then
   exit 1
 fi
 
-cd $INPUT_DIR
-
 if [[ ! -e $CHIP_NAME  ]]
 then
   echo -e "\nERROR: Treatment bed file does not exist"
@@ -92,40 +86,49 @@ then
 fi
 
 # 1) Re-mix ChIP and control bed files
-bash $REMIX_PATH -i $INPUT_DIR -t $CHIP_NAME -c $CONTROL_NAME -o $OUTPUT_DIR -m unequal -b $BOOTSTRAP -s $SEED
+mkdir -p $OUTPUT_DIR
+RECAP_Re-Mix.sh -i $INPUT_DIR -t $CHIP_NAME -c $CONTROL_NAME -o $OUTPUT_DIR -m unequal -b $BOOTSTRAP -s $SEED
 
 # 2) Call original peaks using MACS
 # Please specify your own MACS parameters!
 # NOTE: p-value threshold must be set to 0.1 for MACS
-cd $INPUT_DIR
+mkdir -p $OUTPUT_DIR/MACS_original
 macs2 callpeak -t $CHIP_NAME -c $CONTROL_NAME --pvalue 0.10 -n ${CHIP_NAME%.*} --outdir "$OUTPUT_DIR/MACS_original"
 
 # 3) Call re-mixed peaks using MACS specifying desired parameters
 # Please specify your own MACS parameters!
 # NOTE: p-value threshold must be set to 0.1 for MACS
-cd "$OUTPUT_DIR/re-mix"
+pushd "$OUTPUT_DIR/re-mix"
 for (( i=1; i<=$BOOTSTRAP; i++ ))
 do
   macs2 callpeak -t "${CHIP_NAME%.bed}.bootstrap_$i.bed" -c "${CONTROL_NAME%.bed}.bootstrap_$i.bed" --pvalue 0.10 -n "${CHIP_NAME%.*}.bootstrap_$i" --outdir "$OUTPUT_DIR/MACS_re-mix"
 done
+popd
 
 # All non-MACS summary files in MACS_re-mix must be deleted if $BOOTSTRAP > 1
 if [ -d "$OUTPUT_DIR/MACS_re-mix" ]
 then 
-  cd "$OUTPUT_DIR/MACS_re-mix"
+  pushd "$OUTPUT_DIR/MACS_re-mix"
   find . -type f ! -name '*_peaks.xls' -delete 
+  popd
 else
   echo "Output directory doesn't exist!"
   exit 1
 fi
 
 # 4) Recalibrate original peak p-values using RECAP
 # NOTE: Check for correct header and p-value column if you obtain any errors here
-cd $OUTPUT_DIR
-mkdir MACS_RECAP
-
-perl $PERL_PATH --dirOrig "$OUTPUT_DIR/MACS_original" --nameOrig "${CHIP_NAME%.*}_peaks.xls" --dirRemix "$OUTPUT_DIR/MACS_re-mix" --nameRemix "${CHIP_NAME%.*}" --dirOutput "$OUTPUT_DIR/MACS_RECAP" --nameOutput "${CHIP_NAME%.*}.RECAP.bootstrap_${BOOTSTRAP}_peaks.xls" --bootstrap $BOOTSTRAP --header $HEADER --pvalCol 7 --delim t --software M
-
+mkdir -p $OUTPUT_DIR/MACS_RECAP
+pushd $OUTPUT_DIR
+RECAP.pl \
+  --dirOrig "$(realpath $OUTPUT_DIR/MACS_original)" \
+  --nameOrig "${CHIP_NAME%.*}_peaks.xls" \
+  --dirRemix "$(realpath $OUTPUT_DIR/MACS_re-mix)" \
+  --nameRemix "${CHIP_NAME%.*}" \
+  --dirOutput "$(realpath $OUTPUT_DIR/MACS_RECAP)" \
+  --nameOutput "${CHIP_NAME%.*}.RECAP.bootstrap_${BOOTSTRAP}_peaks.xls" \
+  --bootstrap $BOOTSTRAP --header $HEADER --pvalCol 7 --delim t --software M
+popd
 #################################################################
 ######################## End Script Here ########################
 }
@@ -139,10 +142,10 @@ usage() {
   [Output directory] [Bootstrap]  [Header]
 
  ${bold}USAGE:${normal}
-  -i, --input 	    Input file directory (absolute path)
+  -i, --input 	    Input file directory
   -t, --treatment   Treatment file (full name with extension)
   -c, --control     Control file (full name with extension)
-  -o, --output      Output file directory (absolute path)
+  -o, --output      Output file directory
   -b, --bootstrap   Number of re-mixes
   -e, --header      Header number of peak calling output files
 

diff --git a/RECAP_Re-Mix.sh b/RECAP_Re-Mix.sh
@@ -59,10 +59,10 @@ echo "##################################################"
 echo "######         RECAP RE-MIX  v$VERSION         ######"
 echo "##################################################"
 echo ""
-echo "Input directory  (absolute path):    $INPUT_DIR"
+echo "Input directory:    $INPUT_DIR"
 echo "Treatment library:  $TREATMENT_NAME"
 echo "Control library:    $CONTROL_NAME"
-echo "Output directory (absolute path):   $OUTPUT_DIR"
+echo "Output directory:   $OUTPUT_DIR"
 echo "Re-mix method:      $METHOD_NAME"
 echo "Number of re-mixes: $BOOTSTRAP"
 echo "Random seed: $SEED"
@@ -73,8 +73,6 @@ then
 	exit 1
 fi
 
-cd $INPUT_DIR
-
 if [[ ! -e $TREATMENT_NAME || ! $TREATMENT_NAME == *.bed ]]
 then
 	echo -e "\nERROR: Treatment bed file does not exist"
@@ -97,14 +95,13 @@ fi
 # Base names of treatment and control libraries
 TREATMENT_NAME_BASE="${TREATMENT_NAME%.*}"
 CONTROL_NAME_BASE="${CONTROL_NAME%.*}"
-
+
+mkdir -p $OUTPUT_DIR/re-mix
 for (( BOOTSTRAP_COUNT=1; BOOTSTRAP_COUNT<=$BOOTSTRAP; BOOTSTRAP_COUNT++ ))
 do
-	cd $INPUT_DIR
 	echo ""
 	echo "${bold}Starting Re-Mixing Procedure #$BOOTSTRAP_COUNT ${normal}"
 	echo "Creating directory for re-mix files:"
-	mkdir -p $OUTPUT_DIR/re-mix
 	echo "Check!"
 
 	echo "Concatenating treatment and control libraries"
@@ -117,38 +114,34 @@ do
 		echo "Unequal mixing method selected"
 		FIRST_LINES=$( wc -l < $TREATMENT_NAME )
 		LAST_LINES=$( wc -l < $CONTROL_NAME )
-		cd $OUTPUT_DIR/re-mix
 
 	# If method is equal
 	elif [ $METHOD = 1 ]
 	then
 		echo "Equal mixing method selected"
-		cd $OUTPUT_DIR/re-mix
 		COMBINED_LINES=$(wc -l < $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp)
 		FIRST_LINES=$(( COMBINED_LINES / 2 ))
 		LAST_LINES=$(( COMBINED_LINES - FIRST_LINES ))
 	fi
 
 	echo "Re-mixing..."
-	shuf --random-source=<(get_seeded_random $SEED) -o $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp < $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp
+	shuf --random-source=<(get_seeded_random $SEED) -o $OUTPUT_DIR/re-mix/$TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp < $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp
 	echo "Check!"
 
 	echo "Creating re-mixed treatment library"
-	head -n $FIRST_LINES $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp > $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.bed
+	head -n $FIRST_LINES $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp > $OUTPUT_DIR/re-mix/$TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.bed
 	echo "Check!"
 
 	echo "Creating re-mixed control library"
-	tail -n $LAST_LINES  $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp > $CONTROL_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.bed
+	tail -n $LAST_LINES  $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp > $OUTPUT_DIR/re-mix/$CONTROL_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.bed
 	echo "Check!"
 
 	echo "Deleting temporary files"
-	rm $TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp
+	rm $OUTPUT_DIR/re-mix/$TREATMENT_NAME_BASE.bootstrap_$BOOTSTRAP_COUNT.tmp
 	echo "Check!"
 	echo "Completed re-mix #$BOOTSTRAP_COUNT"
 done
 
-cd $INPUT_DIR
-
 end_time=`date +%s`
 echo RECAP RE-MIX execution time: `expr $end_time - $start_time`s.
 
@@ -165,10 +158,10 @@ usage() {
   [Output directory] [Re-mix method]  [Bootstrap]
 
  ${bold}USAGE:${normal}
-  -i, --input 	    Input file directory (absolute path) 
+  -i, --input 	    Input file directory 
   -t, --treatment   Treatment bed file
   -c, --control     Control bed file
-  -o, --output      Output file directory (absolute path)
+  -o, --output      Output file directory
   -m, --method      Method of re-mixing (equal) or (unequal)
   -b, --bootstrap   Number of re-mixes