Merge pull request #574 from RoanKanninga/master

upgrade to NGS_DNA/3.2.4 + bugfixing
molgenis · Aug 4, 2016 · c36d3f0 · c36d3f0
2 parents 6431642 + 24feafa
commit c36d3f0
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Showing 4 changed files with 15 additions and 18 deletions.
diff --git a/compute5/NGS_Automated/automated_generate_template.sh b/compute5/NGS_Automated/automated_generate_template.sh
@@ -5,7 +5,7 @@ set -u
 
 ### NEEDS 2 arguments! PROJECT AND BATCH
 
-module load NGS_DNA/3.2.3
+module load NGS_DNA/3.2.4
 module list 
 HOST=$(hostname)
 ##Running script for checking the environment variables

diff --git a/compute5/NGS_Automated/copyProjectDataToPrm.sh b/compute5/NGS_Automated/copyProjectDataToPrm.sh
@@ -41,7 +41,7 @@ do
 
         if [ -f ${LOGDIR}/copyProjectDataToPrm.sh.locked ]
         then
-            	exit 0
+            	continue
 	else
 		touch ${LOGDIR}/copyProjectDataToPrm.sh.locked
         fi
@@ -53,7 +53,7 @@ do
 	then
 		countFilesProjectDataDirTmp=$(ls -R ${PROJECTSDIR}/${projectName}/*/results/ | wc -l)
 		module load hashdeep/4.4-foss-2015b
-		if [ ! -f ${PROJECTSDIR}/${projectName}.allResultmd5sums ]
+		if [ ! -f ${PROJECTSDIR}/${projectName}/${projectName}.allResultmd5sums ]
 		then
 			cd ${PROJECTSDIR}/${projectName}/
 			md5deep -r -j0 -o f -l */results/ > ${projectName}.allResultmd5sums

diff --git a/compute5/NGS_Automated/copyRawDataToDiagnosticsCluster.sh b/compute5/NGS_Automated/copyRawDataToDiagnosticsCluster.sh
@@ -106,17 +106,19 @@ do
 			for i in $(ls *.fq.gz.md5 )
 			do
 				if md5sum -c $i
-				then
-					echo "data copied to DiagnosticsCluster" >> $LOGGER
-					printf ".. done \n" >> $LOGGER
-					touch $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster
-					touch ${filePrefix}.md5sums.checked
+				then		
+
+					awk '{print $2" CHECKED, and is correct"}' $i >> $LOGGER
 				else
 					echo "md5sum check failed, the copying will start again" >> $LOGGER
 					rsync -r -a ${copyRawGatToDiagnosticsCluster}
-                                	echo "data copied to DiagnosticsCluster" >> $LOGGER
+					echo -e "data copied to DiagnosticsCluster \n" >> $LOGGER
+
 				fi
 			done
+			touch $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster
+			touch ${filePrefix}.md5sums.checked
+
 		else
 			echo "Retry: Copying data to DiagnosticsCluster" >> $LOGGER
 			rsync -r -a ${copyRawGatToDiagnosticsCluster}

diff --git a/compute5/NGS_Automated/copyRawDataToPrm.sh b/compute5/NGS_Automated/copyRawDataToPrm.sh
@@ -17,10 +17,7 @@ pipeline="dna"
 
 function finish {
 	echo "TRAPPED"
-	if [ -f ${LOGDIR}/copyDataToPrm.sh.locked ]
-	then
-		rm ${LOGDIR}/copyDataToPrm.sh.locked
-	fi
+		rm -f ${LOGDIR}/copyDataToPrm.sh.locked
 }
 trap finish HUP INT QUIT TERM EXIT ERR
 
@@ -87,6 +84,7 @@ do
 
 	if [[ -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster && ! -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToPrm ]]
 	then
+		echo "working on ${filePrefix}"
 		countFilesRawDataDirTmp=$(ls ${RAWDATADIR}/${filePrefix}/${filePrefix}* | wc -l)
 		if [ "${makeRawDataDir}" == "f" ]
 		then
@@ -123,10 +121,7 @@ do
 						echo -e "De data voor project ${filePrefix} is gekopieerd naar ${RAWDATADIRPRM}" | mail -s "${filePrefix} copied to permanent storage" ${ONTVANGER}
 						touch $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToPrm
 					fi
-				  	if [ -f $LOGDIR/${filePrefix}/${filePrefix}.failed ] 
-                                        then
-						rm $LOGDIR/${filePrefix}/${filePrefix}.failed
-					fi
+						rm -f $LOGDIR/${filePrefix}/${filePrefix}.failed
                                 fi
                         else
 				echo "$filePrefix: $countFilesRawDataDirTmp | $countFilesRawDataDirPrm"
@@ -145,7 +140,7 @@ do
 			echo -e "De md5sum checks voor project ${filePrefix} op ${RAWDATADIRPRM} zijn mislukt.De originele data staat op ${HOSTNA}:${RAWDATADIR}\n\nDeze mail is verstuurd omdat er al 10 pogingen zijn gedaan om de data te kopieren/md5summen" | mail -s "${filePrefix} failing to copy to permanent storage" ${ONTVANGER}
 		fi
 	fi
-	rm ${LOGDIR}/copyDataToPrm.sh.locked
+	rm -f ${LOGDIR}/copyDataToPrm.sh.locked
 done<${SAMPLESHEETSDIR}/allSampleSheets_DiagnosticsCluster.txt
 
 trap - EXIT