From b85ca2948eb4f430cf587fe8d56db747ba602341 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Thu, 7 Jul 2016 16:55:53 +0200 Subject: [PATCH] small changes to copyRawDataToPrm.sh --- compute5/NGS_Automated/copyRawDataToPrm.sh | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/compute5/NGS_Automated/copyRawDataToPrm.sh b/compute5/NGS_Automated/copyRawDataToPrm.sh index 089ee93d..5abc3596 100755 --- a/compute5/NGS_Automated/copyRawDataToPrm.sh +++ b/compute5/NGS_Automated/copyRawDataToPrm.sh @@ -47,7 +47,6 @@ do if [ -d ${LOGDIR}/${filePrefix}/ ] then - echo "(copyPrm) everything is finished of ${filePrefix}" continue fi @@ -132,15 +131,15 @@ do mv $LOGDIR/${filePrefix}.copyToPrm.logger $LOGDIR/${filePrefix}/ mv ${LOGDIR}/TMP/${filePrefix}.unique.projects $LOGDIR/${filePrefix}/projects.txt echo "finished with rawdata" >> ${LOGDIR}/${filePrefix}/${filePrefix}.copyToPrm.logger - - logFileStatistics=$(cat ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log) - if [ ${groupname} == "umcg-gaf" ] + if ls ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log 1> /dev/null 2>&1 then - - echo -e "Demultiplex statistics ${filePrefix}: \n\n ${logFileStatistics}" | mail -s "Demultiplex statistics ${filePrefix}" ${GAFmail} + logFileStatistics=$(cat ${RAWDATADIR}/${filePrefix}/${filePrefix}*.log) + if [ ${groupname} == "umcg-gaf" ] + then + echo -e "Demultiplex statistics ${filePrefix}: \n\n ${logFileStatistics}" | mail -s "Demultiplex statistics ${filePrefix}" ${GAFmail} + fi + echo -e "De data voor project ${filePrefix} is gekopieerd naar ${RAWDATADIRPRM}" | mail -s "${filePrefix} copied to permanent storage" ${ONTVANGER} fi - echo -e "De data voor project ${filePrefix} is gekopieerd naar ${RAWDATADIRPRM}" | mail -s "${filePrefix} copied to permanent storage" ${ONTVANGER} - if [ -f $LOGDIR/${filePrefix}.failed ] then rm $LOGDIR/${filePrefix}.failed