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Merge pull request #569 from RoanKanninga/master
putting rawdata logs in the per rawdata folder
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -35,7 +35,7 @@ echo "Logfiles will be written to $LOGDIR" | |
| for line in ${ARR[@]} | ||
| do | ||
| projectName=${line} | ||
| LOGGER=${LOGDIR}/${projectName}.copyProjectDataToPrm.logger | ||
| LOGGER=${LOGDIR}/${projectName}/${projectName}.copyProjectDataToPrm.logger | ||
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| FINISHED="no" | ||
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@@ -49,7 +49,7 @@ do | |
| makeProjectDataDir=$(ssh ${groupname}[email protected] "sh ${PROJECTSDIRPRM}/checkProjectData.sh ${PROJECTSDIRPRM} ${projectName}") | ||
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| copyProjectDataDiagnosticsClusterToPrm="${PROJECTSDIR}/${projectName}/* ${groupname}[email protected]:${PROJECTSDIRPRM}/${projectName}" | ||
| if [[ -f $LOGDIR/${projectName}/${projectName}.pipeline.finished && ! -f $LOGDIR/${projectName}/${projectName}.projectDataCopiedToPrm ]] | ||
| if [[ -d $LOGDIR/${projectName}/ && ! -f $LOGDIR/${projectName}/${projectName}.projectDataCopiedToPrm ]] | ||
| then | ||
| countFilesProjectDataDirTmp=$(ls -R ${PROJECTSDIR}/${projectName}/*/results/ | wc -l) | ||
| module load hashdeep/4.4-foss-2015b | ||
|
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@@ -76,19 +76,16 @@ do | |
| then | ||
| echo "md5sum check failed, the copying will start again" >> ${LOGGER} | ||
| rsync -r -av --exclude rawdata/ ${copyProjectDataDiagnosticsClusterToPrm} >> $LOGGER 2>&1 | ||
| echo "copy failed" >> $LOGDIR/${projectName}.copyProjectDataToPrm.failed | ||
| echo "copy failed" >> $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed | ||
| elif [[ "${COPIEDTOPRM}" == *"PASS"* ]] | ||
| then | ||
| touch $LOGDIR/${projectName}.projectDataCopiedToPrm | ||
| touch $LOGDIR/${projectName}/${projectName}.projectDataCopiedToPrm | ||
| echo "finished copying project data to calculon" >> ${LOGGER} | ||
| printf "De project data voor project ${projectName} is gekopieerd naar ${PROJECTSDIRPRM}" | mail -s "project data for project ${projectName} is copied to permanent storage" ${ONTVANGER} | ||
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| mv $LOGDIR/${projectName}.projectDataCopiedToPrm $LOGDIR/${projectName}/ | ||
| mv $LOGDIR/${projectName}.copyProjectDataToPrm.logger $LOGDIR/${projectName}/ | ||
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| if [ -f $LOGDIR/${projectName}.copyProjectDataToPrm.failed ] | ||
| if [ -f $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed ] | ||
| then | ||
| rm $LOGDIR/${projectName}.copyProjectDataToPrm.failed | ||
| rm $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed | ||
| fi | ||
| fi | ||
| else | ||
|
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@@ -98,9 +95,9 @@ do | |
| fi | ||
| fi | ||
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| if [ -f $LOGDIR/${projectName}.copyProjectDataToPrm.failed ] | ||
| if [ -f $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed ] | ||
| then | ||
| COUNT=$(cat $LOGDIR/${projectName}.copyProjectDataToPrm.failed | wc -l) | ||
| COUNT=$(cat $LOGDIR/${projectName}/${projectName}.copyProjectDataToPrm.failed | wc -l) | ||
| if [ $COUNT == 10 ] | ||
| then | ||
| HOSTNA=$(hostname) | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -35,7 +35,7 @@ for line in ${ARR[@]} | |
| do | ||
| csvFile=$(basename $line) | ||
| filePrefix="${csvFile%.*}" | ||
| LOGGER=${LOGDIR}/${filePrefix}.copyToPrm.logger | ||
| LOGGER=${LOGDIR}/${filePrefix}/${filePrefix}.copyToPrm.logger | ||
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| FINISHED="no" | ||
| OLDIFS=$IFS | ||
|
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@@ -45,11 +45,6 @@ do | |
| run=$3 | ||
| IFS=$OLDIFS | ||
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| if [ -d ${LOGDIR}/${filePrefix}/ ] | ||
| then | ||
| continue | ||
| fi | ||
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| if [ -f ${LOGDIR}/copyDataToPrm.sh.locked ] | ||
| then | ||
| echo "copyToPrm is locked" | ||
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@@ -61,12 +56,6 @@ do | |
| ##get header to decide later which column is project | ||
| HEADER=$(head -1 ${line}) | ||
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| if [ -d ${LOGDIR}/${filePrefix}/ ] | ||
| then | ||
| echo "(startPipeline) everything is finished of ${filePrefix}" | ||
| continue | ||
| fi | ||
|
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| ##Remove header, only want to keep samples | ||
| sed '1d' $line > ${LOGDIR}/TMP/${filePrefix}.utmp | ||
| OLDIFS=$IFS | ||
|
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@@ -96,7 +85,7 @@ do | |
| copyRawDiagnosticsClusterToPrm="${RAWDATADIR}/${filePrefix}/* ${groupname}[email protected]:${RAWDATADIRPRM}/${filePrefix}" | ||
| makeRawDataDir=$(ssh ${groupname}[email protected] "sh ${RAWDATADIRPRM}/../checkRawData.sh ${RAWDATADIRPRM} ${filePrefix}") | ||
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| if [[ -f $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster && ! -f $LOGDIR/${filePrefix}.dataCopiedToPrm ]] | ||
| if [[ -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToDiagnosticsCluster && ! -f $LOGDIR/${filePrefix}/${filePrefix}.dataCopiedToPrm ]] | ||
| then | ||
| countFilesRawDataDirTmp=$(ls ${RAWDATADIR}/${filePrefix}/${filePrefix}* | wc -l) | ||
| if [ "${makeRawDataDir}" == "f" ] | ||
|
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@@ -115,22 +104,20 @@ do | |
| then | ||
| echo "md5sum check failed, the copying will start again" >> ${LOGGER} | ||
| rsync -r -av ${copyRawDiagnosticsClusterToPrm} >> $LOGGER 2>&1 | ||
| echo "copy failed" >> $LOGDIR/${filePrefix}.failed | ||
| echo "copy failed" >> $LOGDIR/${filePrefix}/${filePrefix}.failed | ||
| elif [[ "${COPIEDTOPRM}" == *"PASS"* ]] | ||
| then | ||
| scp ${SAMPLESHEETSDIR}/${csvFile} ${groupname}[email protected]:${RAWDATADIRPRM}/${filePrefix}/ | ||
| scp ${SAMPLESHEETSDIR}/${csvFile} ${groupname}[email protected]:${SAMPLESHEETSPRMDIR} | ||
| echo "finished copying data to calculon" >> ${LOGGER} | ||
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| mkdir $LOGDIR/${filePrefix}/ | ||
| echo "Moving ${filePrefix} logfiles to $LOGDIR/${filePrefix}/ and removing tmp finished files" >> $LOGGER | ||
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| rm $LOGDIR/${filePrefix}.SampleSheetCopied | ||
| rm $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster | ||
| mv $LOGDIR/${filePrefix}.copyToDiagnosticsCluster.logger $LOGDIR/${filePrefix}/ | ||
| mv $LOGDIR/${filePrefix}.copyToPrm.logger $LOGDIR/${filePrefix}/ | ||
| mv ${LOGDIR}/TMP/${filePrefix}.unique.projects $LOGDIR/${filePrefix}/projects.txt | ||
| #rm $LOGDIR/${filePrefix}.SampleSheetCopied | ||
| #rm $LOGDIR/${filePrefix}.dataCopiedToDiagnosticsCluster | ||
| #mv $LOGDIR/${filePrefix}.copyToDiagnosticsCluster.logger $LOGDIR/${filePrefix}/ | ||
| #mv $LOGDIR/${filePrefix}.copyToPrm.logger $LOGDIR/${filePrefix}/ | ||
| #mv ${LOGDIR}/TMP/${filePrefix}.unique.projects $LOGDIR/${filePrefix}/projects.txt | ||
| echo "finished with rawdata" >> ${LOGDIR}/${filePrefix}/${filePrefix}.copyToPrm.logger | ||
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| if ls ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log 1> /dev/null 2>&1 | ||
| then | ||
| logFileStatistics=$(cat ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log) | ||
|
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@@ -140,9 +127,9 @@ do | |
| fi | ||
| echo -e "De data voor project ${filePrefix} is gekopieerd naar ${RAWDATADIRPRM}" | mail -s "${filePrefix} copied to permanent storage" ${ONTVANGER} | ||
| fi | ||
| if [ -f $LOGDIR/${filePrefix}.failed ] | ||
| if [ -f $LOGDIR/${filePrefix}/${filePrefix}.failed ] | ||
| then | ||
| rm $LOGDIR/${filePrefix}.failed | ||
| rm $LOGDIR/${filePrefix}/${filePrefix}.failed | ||
| fi | ||
| fi | ||
| else | ||
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@@ -153,9 +140,9 @@ do | |
| fi | ||
| fi | ||
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| if [ -f $LOGDIR/${filePrefix}.failed ] | ||
| if [ -f $LOGDIR/${filePrefix}/${filePrefix}.failed ] | ||
| then | ||
| COUNT=$(cat $LOGDIR/${filePrefix}.failed | wc -l) | ||
| COUNT=$(cat $LOGDIR/${filePrefix}/${filePrefix}.failed | wc -l) | ||
| if [ $COUNT == 10 ] | ||
| then | ||
| HOSTNA=$(hostname) | ||
|
|
||
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