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Slightly better output now -- no longer emitting pdfs by default. Emails will go to gsamembers now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5224 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-10 13:02:24 +00:00
parent 947cc44854
commit b1e4e1afb6
1 changed files with 13 additions and 18 deletions
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31
shell/runGATKReport.csh
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@ -13,39 +13,34 @@ setenv ARCHIVE $ARCHIVE_DIR/$DATE
setenv SUMMARY $SUMMARY_DIR/$DATE
setenv GATK ~/dev/GenomeAnalysisTK/trunk
setenv GATK_RELEASE_VERSION `ls -l /humgen/gsa-hpprojects/GATK/bin/current | sed 's/.*GenomeAnalysisTK-//'`
setenv REPORT_TXT $DIR/report.txt
rm -f report.txt
rm -f $REPORT_TXT
cd $DIR
echo "\n####################\nArchiving recently submitted jobs" >> report.txt
python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D >> report.txt
echo "\n####################\nArchiving recently submitted jobs" >> $REPORT_TXT
python $GATK/python/analyzeRunReports.py archive $DIR/submitted -o $ARCHIVE.gz -D >> $REPORT_TXT
echo "Released version, all runs" >> report.txt
#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 "\n####################\nReleased version, all runs" >> $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 "\n####################\nAll runs" >> report.txt
python $GATK/python/analyzeRunReports.py summary $ARCHIVE.gz --max_days 1 >> report.txt
python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE.gz -E sting --max_days 1 >> report.txt
echo "\n####################\nLast day, all versions" >> report.txt
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
echo "\n####################\nLast day, all versions" >> $REPORT_TXT
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
#echo "Archive directory contents"
#du -sh $ARCHIVE_DIR
if (1 == 1) then
if (1 == 0) then
foreach maxDays ( 30 360 )
echo "Creating table"
setenv table $ARCHIVE.${maxDays}_days.table
python $GATK/python/analyzeRunReports.py table $ARCHIVE_DIR/*.gz -o $table --max_days $maxDays
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"
python $GATK/python/analyzeRunReports.py exceptions $ARCHIVE_DIR/*.gz -o $SUMMARY.${maxDays}_days.sting.exceptions.txt --max_days $maxDays -E sting --no-dev
@ -56,5 +51,5 @@ 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
cat $REPORT_TXT | mutt -a $REPORT_TXT -a $SUMMARY.30_days.pdf -a $SUMMARY.360_days.pdf -s "GATK run report for $DATE" gsamembers