93 líneas
2.6 KiB
Bash
93 líneas
2.6 KiB
Bash
#REMcMaster.sh Is to perform all REMc task and to operate from source directory REMc
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#Step 0 Perform JoinInteractExps3dev.R to create the "REMcRdy_lm_only.csv" and "Shift_only.csv" files
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Rscript JoinInteractExps3dev.R
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#Step1 Perform REMc java utility using file input file REMcRdy_lm_only.csv
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#and producing REMcRdy_lm_only.csv-finalTable.csv
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sh ./REMcJar2.sh
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wait #wait isn't holding process until Jar is complete. Should take at least 3minuites
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#Step 2
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if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
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echo "REMcRdy_lm_only.csv-finalTable.csv exists."
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#Jarflag= 1
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#echo "Jarflag = $Jarflag"
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echo "REMcJar... .sh completed"
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else
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echo "REMcJar failed"
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wait
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exit
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fi
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echo "start Step2"
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#Step2 If REMcJar successfully produces "REMcRdy_lm_only.csv-finalTable.csv"
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#then add shift values back to the "REMcRdy_lm_only.csv-finalTable.csv"
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#and output it as "REMcWithShift.csv" to be used to produce the REMc Heatmaps.
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if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
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echo "REMcRdy_lm_only.csv-finalTable.csv exists."
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Rscript ./AddShiftVals2.R
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wait
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echo "AddShiftVals2.R executed"
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wait
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fi
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#Step3 Execute REMcHeatmaps_zscores.R contingent upon "REMcWithShift.csv" being created.
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cd REMcHeatmaps
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if [ -f "REMcWithShift.csv" ]; then
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echo "REMcWithShift.csv exists."
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fi
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cd ..
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Rscript REMcHeatmaps_zscores.R
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wait
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echo "REMcHeatmaps executed"
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wait
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pdftk *.pdf output compiledREMcHeatmaps.pdf
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wait
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#Step4 Begin the process of GTF contingent upon "REMcRdy_lm_only.csv-finalTable.csv"
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# being produced by "REMcJar.sh" (Step1)
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if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
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echo "REMcRdy_lm_only.csv-finalTable.csv exists."
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python2 DconJG2.py REMcRdy_lm_only.csv-finalTable.csv GTF/Process/
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#python2 DconJG.py REMcRdy_lm_only.csv-finalTable.csv 12 GTF/Process/
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else
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echo "DconJG.py failed"
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wait
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exit
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fi
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if [ -f "GTF/Process/REMcRdy_lm_only/1-0-0-finaltable.csv" ]; then
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echo "Begin copying REMcRdy_lm_only to /Function and /Component"
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cp -r GTF/Process/REMcRdy_lm_only GTF/Function/
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echo "Copy to Function complete"
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wait
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cp -r GTF/Process/REMcRdy_lm_only GTF/Component/
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echo "Copy to Component complete"
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wait
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else
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echo "COPY failed"
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wait
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exit
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fi
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if [ -f "GTF/Function/REMcRdy_lm_only/1-0-0-finaltable.csv" ]; then
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echo "Begin concurrent running of GTF tasks"
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sh ./mProcess.sh &
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sh ./mFunction.sh &
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sh ./mComponent.sh &
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echo "GTF ontologies run in background"
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wait
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else
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echo "GTFontologies failed"
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exit
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echo "masterDev.sh Finished"
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exit
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fi
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