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Better run reporting structure. Now text report is attached as well as inline in the email, so you can easily view it in fix width fonts! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5158 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-01 12:58:48 +00:00
parent 393df46055
commit d9532ecf53
1 changed files with 27 additions and 13 deletions
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40
shell/runGATKReport.csh
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@ -12,29 +12,40 @@ setenv DATE `date +"%m_%d_%Y"`
setenv ARCHIVE $ARCHIVE_DIR/$DATE setenv ARCHIVE $ARCHIVE_DIR/$DATE
setenv SUMMARY $SUMMARY_DIR/$DATE setenv SUMMARY $SUMMARY_DIR/$DATE
setenv GATK ~/dev/GenomeAnalysisTK/trunk setenv GATK ~/dev/GenomeAnalysisTK/trunk
setenv GATK_RELEASE_VERSION `ls -l /humgen/gsa-hpprojects/GATK/bin/current | sed 's/.*GenomeAnalysisTK-//'`
rm -f report.txt
cd $DIR cd $DIR
echo "Archiving recently submitted jobs" echo "\n####################\nArchiving recently submitted jobs" >> report.txt
python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D #python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D >> report.txt
echo "All runs" echo "Released version, all runs" >> report.txt
python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 #python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --rev $GATK_RELEASE_VERSION >> report.txt
#python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --rev $GATK_RELEASE_VERSION >> report.txt
python $GATK/python/analyzeRunReports.py summary $ARCHIVE_DIR/*.gz --rev $GATK_RELEASE_VERSION >> report.txt
python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -E sting --rev $GATK_RELEASE_VERSION >> report.txt
echo "No-dev" echo "\n####################\nAll runs" >> report.txt
python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 --no-dev python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 >> report.txt
python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz --max_days 1 -E sting --no-dev python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --max_days 1 >> report.txt
echo "Archive directory contents" echo "\n####################\nLast day, all versions" >> report.txt
du -sh $ARCHIVE_DIR python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 --no-dev >> report.txt
python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz --max_days 1 -E sting --no-dev >> report.txt
foreach maxDays ( 7 30 360 ) #echo "Archive directory contents"
#du -sh $ARCHIVE_DIR
if (1 == 1) then
foreach maxDays ( 30 360 )
echo "Creating table" echo "Creating table"
setenv table $ARCHIVE.${maxDays}_days.table setenv table $ARCHIVE.${maxDays}_days.table
python $GATK/python/analyzeRunReports.py table $ARCHIVE_DIR/*.gz -o $table --max_days $maxDays python $GATK/python/analyzeRunReports.py table $ARCHIVE_DIR/*.gz -o $table --max_days $maxDays
echo "Creating summary" echo "Creating summary"
Rscript $GATK/R/GATKRunReport.R $table $SUMMARY.${maxDays}_days.pdf "of previous $maxDays days" Rscript $GATK/R/GATKRunReport.R $table $SUMMARY.${maxDays}_days.pdf "of previous $maxDays days"
echo "Creating exception report" echo "Creating exception report"
python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -o $SUMMARY.${maxDays}_days.sting.exceptions.txt --max_days $maxDays -E sting --no-dev python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -o $SUMMARY.${maxDays}_days.sting.exceptions.txt --max_days $maxDays -E sting --no-dev
@ -42,5 +53,8 @@ foreach maxDays ( 7 30 360 )
rm $table rm $table
end end
endif
#echo "GATK daily run report" | mutt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK Run report PDFs for $DATE" gsamembers
cat report.txt | mutt -a report.txt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK run report for $DATE" depristo
echo "GATK daily run report" | mutt -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -a $SUMMARY.7_days.pdf -s "GATK Run report PDFs for $DATE" gsamembers