Merge pull request #456 from RoanKanninga/3.2.3

improved the copy prmtotmp data + bugfix in CheckIlluminaEncoding
molgenis · Mar 8, 2016 · 6e55bc0 · 6e55bc0
2 parents 7f909e8 + eab474b
commit 6e55bc0
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Showing 2 changed files with 34 additions and 19 deletions.
diff --git a/compute5/NGS_DNA/protocols/CheckIlluminaEncoding.sh b/compute5/NGS_DNA/protocols/CheckIlluminaEncoding.sh
@@ -16,21 +16,21 @@ checkIlluminaEncoding() {
 barcodeFqGz=$1
 echo ${barcodeFqGz}
 
-Lines=(`zcat ${barcodeFqGz} | head -96 | awk 'NR % 4 == 0'`)
+lines=(`zcat ${barcodeFqGz} | head -96 | awk 'NR % 4 == 0'`)
 count=1
 nodecision=0
 numberoflines=0
-for line in  ${Lines[*]}
+for line in  ${lines[@]}
 do
-	numberoflines=$(( numberoflines++ ))
+	numberoflines=$(( numberoflines+1 ))
 	#check for illumina encoding 1.5
 	if [[ "$line" =~ [P-Z] ]] || [[ "$line" =~ [a-g] ]]
 		then
         	encoding="1.5"
 	        if [[ ${count} -eq 1 ]]
         	then
             	lastEncoding=${encoding}
-            	count=$(( count++ ))
+            	count=$(( count+1 ))
         	fi
 
         	if ! [ "${encoding}" == "${lastEncoding}" ]
@@ -49,7 +49,7 @@ do
 	        if [[ ${count} -eq 1 ]]
         	then
         		lastEncoding=${encoding}
-	        	count=$(( count++ ))
+	        	count=$(( count+1 ))
         	fi
         	if ! [ "${encoding}" == "${lastEncoding}" ]
         	then
@@ -61,7 +61,7 @@ do
               	lastEncoding="${encoding}"
 	elif [[ "$line" =~ @ ]] || [[ "$line" =~ [A-J] ]]
         	then
-                nodecision=$(( nodecision++ ))
+                nodecision=$(( nodecision+1 ))
 	else
 		echo "The encoding is not matching to anything, check FastQ documentation (count=$count)"
 	fi

diff --git a/compute5/NGS_DNA/protocols/CopyPrmTmpData.sh b/compute5/NGS_DNA/protocols/CopyPrmTmpData.sh
@@ -25,25 +25,36 @@ for ((samplenumber = 0; samplenumber <= max_index; samplenumber++))
 do
 
 	RUNNAME=${sequencingStartDate[samplenumber]}_${sequencer[samplenumber]}_${run[samplenumber]}_${flowcell[samplenumber]}	
-	PRMDATADIR=${allRawNgsPrmDataDir}/${RUNNAME}
+	WHOAMI=$(whoami)
+	HOST=$(hostname)
+	if [ "$HOST" == "zinc-finger.gcc.rug.nl" ] && [ ! -d /groups/umcg-gaf/prm02 ]
+	then
+			echo "${WHOAMI}@calculon.hpc.rug.nl:${allRawNgsPrmDataDir}/${RUNNAME}"
+			PRMDATADIR="${WHOAMI}@calculon.hpc.rug.nl:${allRawNgsPrmDataDir}/${RUNNAME}"
+	else	
+			PRMDATADIR=${allRawNgsPrmDataDir}/${RUNNAME}
+	fi
+
 	TMPDATADIR=${allRawNgsTmpDataDir}/${RUNNAME}
 
 	if [[ ${seqType[samplenumber]} == "SR" ]]
 	then
   		mkdir -p ${TMPDATADIR}
 		if [[ ${barcode[samplenumber]} == "None" ]]
 		then
-			rsync -a -r --no-perms \
+			echo "copying ${RUNNAME}_L${lane[samplenumber]}.fq.gz..." 
+			rsync -a -r --no-perms --no-owner \
 			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}.fq.gz \
 			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}.fq.gz
-			rsync -a -r --no-perms \
+			rsync -a -r --no-perms --no-owner \
 			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}.fq.gz.md5 \
 			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}.fq.gz.md5
 		else
-			rsync -a -r --no-perms \
+			echo "copying ${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}.fq.gz..." 
+			rsync -a -r --no-perms --no-owner \
 			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}.fq.gz \
 			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}.fq.gz
-			rsync -a -r --no-perms \
+			rsync -a -r --no-perms --no-owner \
 			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}.fq.gz.md5 \
 			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}.fq.gz.md5	
 		fi
@@ -52,29 +63,33 @@ do
 		mkdir -p ${TMPDATADIR}
 		if [[ ${barcode[samplenumber]} == "None" ]]
     		then
-    		rsync -a -r --no-perms \
+		echo "copying ${RUNNAME}_L${lane[samplenumber]}_1.fq.gz..." 
+    		rsync -a -r --no-perms --no-owner \
     			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_1.fq.gz \
     			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_1.fq.gz
-		rsync -a -r --no-perms \
+		echo "copying ${RUNNAME}_L${lane[samplenumber]}_2.fq.gz..." 
+		rsync -a -r --no-perms --no-owner \
 			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_2.fq.gz \
 			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_2.fq.gz
-		rsync -a -r --no-perms \
+		rsync -a -r --no-perms --no-owner \
 			${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_1.fq.gz.md5 \
 			${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_1.fq.gz.md5
-        	rsync -a -r --no-perms \
+        	rsync -a -r --no-perms --no-owner \
         		${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_2.fq.gz.md5 \
         		${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_2.fq.gz.md5
 		else          
-        	rsync -a -r --no-perms \
+		echo "copying ${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_1.fq.gz..." 
+        	rsync -a -r --no-perms --no-owner \
         		${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_1.fq.gz \
         		${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_1.fq.gz
-        	rsync -a -r --no-perms \
+		echo "copying ${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_2.fq.gz..." 
+        	rsync -a -r --no-perms --no-owner \
         		${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_2.fq.gz \
         		${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_2.fq.gz
-        	rsync -a -r --no-perms \
+        	rsync -a -r --no-perms --no-owner \
         		${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_1.fq.gz.md5 \
         		${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_1.fq.gz.md5
-        	rsync -a -r --no-perms \
+        	rsync -a -r --no-perms --no-owner \
         		${PRMDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_2.fq.gz.md5 \
         		${TMPDATADIR}/${RUNNAME}_L${lane[samplenumber]}_${barcode[samplenumber]}_2.fq.gz.md5
     		fi