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Merge pull request #105 from RoanKanninga/master
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updated some echo commands + removed unnecesessary check
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@Gerbenvandervries
Gerbenvandervries committed Feb 15, 2016
2 parents 8a96ab4 + cd6bf18 commit 7b60297
Showing 1 changed file with 53 additions and 68 deletions.
121 changes: 53 additions & 68 deletions automate_demultiplexing/automate.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -26,87 +26,71 @@ do
run=$3
IFS=$OLDIFS
## Check if there the run is already completed
if [ -f ${NEXTSEQDIR}/${PROJECTNAME}/RunCompletionStatus.xml ]
if [ -f ${NEXTSEQDIR}/${PROJECTNAME}/RunCompletionStatus.xml ]
then
### Check if data is already demultiplexed
echo "(${PROJECTNAME}) Check if data is demultiplexed" >> ${DEBUGGER}
if [ ! -f ${NEXTSEQDIR}/${PROJECTNAME}_Demultiplexing.finished ]
then
echo "Check if the demultiplexing is already started" >> ${DEBUGGER}
### Check if the demultiplexing is already started
if [ ! -f ${LOGSDIR}/${PROJECTNAME}_Demultiplexing.started ]
then
### Check if the demultiplexing is already started
if [ ! -f ${LOGSDIR}/${PROJECTNAME}_Demultiplexing.started ]
then
### Check if Samplesheet is there
echo "(${PROJECTNAME}) Check if Samplesheet is there" >> ${DEBUGGER}
if [ -f ${SAMPLESHEETDIR}/${PROJECTNAME}.csv ]
then
echo "Check samplesheet" >> ${DEBUGGER}
python $EBROOTNGSMINUTILS/automate_demultiplexing/checkSampleSheet.py --input ${SAMPLESHEETDIR}/${PROJECTNAME}.csv
if [ $? == 1 ]
then
echo "There is something wrong in the samplesheet! Exiting" >> ${DEBUGGER}
exit 1
else
#####
## RUN PIPELINE PART ##
#####
RUNFOLDER="run_${run}_${sequencer}"
LOGGERPIPELINE=${WORKDIR}/generatedscripts/${RUNFOLDER}/logger.txt
echo "All checks are done. Logging from now on can be found: ${LOGGERPIPELINE}" >> ${DEBUGGER}
if [ -f ${SAMPLESHEETDIR}/${PROJECTNAME}.csv ]
then
python $EBROOTNGSMINUTILS/automate_demultiplexing/checkSampleSheet.py --input ${SAMPLESHEETDIR}/${PROJECTNAME}.csv
if [ $? == 1 ]
then
echo "There is something wrong in the samplesheet! Exiting" >> ${DEBUGGER}
exit 1
else
echo "Samplesheet is OK" >> ${DEBUGGER}
#####
## RUN PIPELINE PART ##
#####
RUNFOLDER="run_${run}_${sequencer}"
LOGGERPIPELINE=${WORKDIR}/generatedscripts/${RUNFOLDER}/logger.txt
echo "All checks are done. Logging from now on can be found: ${LOGGERPIPELINE}" >> ${DEBUGGER}

## Check if Check file (if samplesheet is already there) is existing
if [ -f ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt ]
then
## Remove tmp Check file
rm ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt
echo "rm ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt" >> ${LOGGERPIPELINE}
fi
### Check if runfolder already exists
if [ ! -d ${WORKDIR}/generatedscripts/$RUNFOLDER ]
then
mkdir -p ${WORKDIR}/generatedscripts/${RUNFOLDER}/
echo "mkdir -p ${WORKDIR}/generatedscripts/${RUNFOLDER}/" >> ${LOGGERPIPELINE}
fi
## Check if Check file (if samplesheet is already there) is existing
if [ -f ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt ]
then
## Remove tmp Check file
rm ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt
echo "rm ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt" >> ${LOGGERPIPELINE}
fi
### Check if runfolder already exists
if [ ! -d ${WORKDIR}/generatedscripts/$RUNFOLDER ]
then
mkdir -p ${WORKDIR}/generatedscripts/${RUNFOLDER}/
echo "mkdir -p ${WORKDIR}/generatedscripts/${RUNFOLDER}/" >> ${LOGGERPIPELINE}
fi

## Direct to generatedscripts folder
cd ${WORKDIR}/generatedscripts/${RUNFOLDER}/
## Direct to generatedscripts folder
cd ${WORKDIR}/generatedscripts/${RUNFOLDER}/

## Copy generate script and samplesheet
cp ${SAMPLESHEETDIR}/${PROJECTNAME}.csv run_${run}_${sequencer}.csv
echo "copied ${SAMPLESHEETDIR}/${PROJECTNAME}.csv to run_${run}_${sequencer}.csv" >> ${LOGGERPIPELINE}
## Copy generate script and samplesheet
cp ${SAMPLESHEETDIR}/${PROJECTNAME}.csv run_${run}_${sequencer}.csv
echo "copied ${SAMPLESHEETDIR}/${PROJECTNAME}.csv to run_${run}_${sequencer}.csv" >> ${LOGGERPIPELINE}

cp ${EBROOTNGS_DEMULTIPLEX}/generate_template.sh ./
echo "Copied ${EBROOTNGS_DEMULTIPLEX}/generate_template.sh to ." >> ${LOGGERPIPELINE}
echo "" >> ${LOGGERPIPELINE}
cp ${EBROOTNGS_DEMULTIPLEX}/generate_template.sh ./
echo "Copied ${EBROOTNGS_DEMULTIPLEX}/generate_template.sh to ." >> ${LOGGERPIPELINE}
echo "" >> ${LOGGERPIPELINE}

### Generating scripts
echo "Generated scripts" >> ${LOGGERPIPELINE}
sh generate_template.sh ${sequencer} ${run}
echo "cd ${WORKDIR}/runs/${RUNFOLDER}/jobs" >> ${LOGGERPIPELINE}
cd ${WORKDIR}/runs/${RUNFOLDER}/jobs
### Generating scripts
echo "Generated scripts" >> ${LOGGERPIPELINE}
sh generate_template.sh ${sequencer} ${run}
echo "cd ${WORKDIR}/runs/${RUNFOLDER}/jobs" >> ${LOGGERPIPELINE}
cd ${WORKDIR}/runs/${RUNFOLDER}/jobs

sh submit.sh
echo "jobs submitted, pipeline is running" >> ${LOGGERPIPELINE}
touch ${LOGSDIR}/${PROJECTNAME}_Demultiplexing.started
echo "De demultiplexing pipeline is gestart, over een aantal uren zal dit klaar zijn \
en word de data automatisch naar zinc-finger gestuurd, hierna word de pipeline gestart" | mail -s "Het demultiplexen van ug is gestart op (`date +%d/%m/%Y` `date +%H:%M`)" ${ONTVANGER}
fi
sh submit.sh
echo "jobs submitted, pipeline is running" >> ${LOGGERPIPELINE}
touch ${LOGSDIR}/${PROJECTNAME}_Demultiplexing.started
echo "De demultiplexing pipeline is gestart, over een aantal uren zal dit klaar zijn \
en word de data automatisch naar zinc-finger gestuurd, hierna word de pipeline gestart" | mail -s "Het demultiplexen van ug is gestart op (`date +%d/%m/%Y` `date +%H:%M`)" ${ONTVANGER}
fi
else
## Do nothing
echo "(${PROJECTNAME}) Check if Samplesheet is there --> Do nothing" >> ${DEBUGGER}
echo "(${PROJECTNAME}) Do nothing" >> ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt
echo "Samplesheet is missing, after 10 times a mail will be send to the user" >> ${DEBUGGER}
echo "Samplesheet is not available" >> ${SAMPLESHEETDIR}/${PROJECTNAME}_Check.txt
fi
else
# Data is already demultiplexed
echo "(${PROJECTNAME}) Data is already demultiplexed" >> ${DEBUGGER}

fi
else
### Run is not completed yet
echo "(${PROJECTNAME}) Run is not completed yet" >> ${DEBUGGER}
fi
done
if [ -f /groups/umcg-gaf/tmp05/Samplesheets/${PROJECTNAME}_Check.txt ]
then
COUNT=$(cat /groups/umcg-gaf/tmp05/Samplesheets/${PROJECTNAME}_Check.txt | wc -l)
Expand All @@ -116,3 +100,4 @@ then
echo "mail has been sent to ${ONTVANGER}"
fi
fi
done

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