File refactoring

workflow/.old/templates/qhtcp/REMcMaster3.sh

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+#REMcMaster.sh Is to perform all REMc task and to operate from source directory REMc
+# Gain permissions to the perl scripts for GTF
+currentDir="$PWD"
+GTFpath="$currentDir/GTF"
+chmod -R u+rwx "$GTFpath"
+#Step 0 Perform JoinInteractExps3dev.R to create the "REMcRdy_lm_only.csv" and "Shift_only.csv" files
+Rscript JoinInteractExps3dev.R 
+
+#Step1 Perform REMc java utility using file input file REMcRdy_lm_only.csv 
+#and producing REMcRdy_lm_only.csv-finalTable.csv
+sh ./REMcJar2.sh
+wait
+#wait isn't holding process until Jar is complete. Should take at least 3minuites
+
+#Step 2 
+if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
+    echo "REMcRdy_lm_only.csv-finalTable.csv exists."
+    #Jarflag= 1
+    #echo "Jarflag =  $Jarflag"
+echo "REMcJar... .sh completed"
+else
+echo "REMcJar failed"
+wait
+exit
+fi
+echo "start Step2"
+#Step2 If REMcJar successfully produces "REMcRdy_lm_only.csv-finalTable.csv" 
+  #then add shift values back to the "REMcRdy_lm_only.csv-finalTable.csv"
+  #and output it as "REMcWithShift.csv" to be used to produce the REMc Heatmaps.
+if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
+    echo "REMcRdy_lm_only.csv-finalTable.csv exists."
+    Rscript ./AddShiftVals2.R 
+    wait
+    echo "AddShiftVals2.R executed"
+ fi
+
+#Step3 Execute REMcHeatmaps_zscores.R contingent upon "REMcWithShift.csv" being created.
+cd REMcHeatmaps
+if [ -f "REMcWithShift.csv" ]; then
+      echo "REMcWithShift.csv exists."
+fi
+
+rm *.pdf  #Remove .pdf files to be sure of a clean 'slate'
+
+cd ..
+      Rscript REMcHeatmaps_zscores.R
+      echo "REMcHeatmaps executed"
+      wait
+cd REMcHeatmaps
+            pdftk *.pdf output compiledREMcHeatmaps.pdf
+
+#Step3b Execute REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R contingent upon "REMcWithShift.csv" being created in ../REMcHeatmapsWithHomology.
+#cp ./Homology/REMcWithShift.csv ./REMcHeatmapsWithHomology/REMcWithShift.csv
+cp ./REMcWithShift.csv ../REMcHeatmapsWithHomology/
+cd ../REMcHeatmapsWithHomology
+if [ -f "REMcWithShift.csv" ]; then
+      echo "REMcWithShift.csv exists."
+fi
+      rm ./Homology/*.pdf  #Remove .pdf files to be sure of a clean 'slate'
+      rm ./Homology/*.csv  #Remove .csv files to be sure of a clean 'slate'
+
+      Rscript REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R REMcWithShift.csv Homology 17_0503_DAmPs_Only.txt Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv
+    
+      echo "REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R executed"
+      wait
+cd Homology
+      pdftk *.pdf output compiledREMcHomologyHeatmaps.pdf
+      
+echo "pdftk executed"
+cd ../..
+    
+#Step4 Begin the process of GTF contingent upon "REMcRdy_lm_only.csv-finalTable.csv"
+# being produced by "REMcJar.sh" (Step1)
+if [ -f "REMcRdy_lm_only.csv-finalTable.csv" ]; then
+    echo "REMcRdy_lm_only.csv-finalTable.csv exists."
+     python3 DconJG2.py REMcRdy_lm_only.csv-finalTable.csv GTF/Process/
+    #python2 DconJG.py REMcRdy_lm_only.csv-finalTable.csv 12 GTF/Process/
+else
+    echo "DconJG2.py failed"
+    wait
+    exit
+
+fi
+
+if [ -f "GTF/Process/REMcRdy_lm_only/1-0-0-finaltable.csv" ]; then
+  echo "Begin copying REMcRdy_lm_only to /Function and /Component"
+  cp -r GTF/Process/REMcRdy_lm_only GTF/Function/
+  echo "Copy to Function complete"
+  wait
+  cp -r GTF/Process/REMcRdy_lm_only GTF/Component/
+  echo "Copy to Component complete"
+
+  wait
+
+else
+    echo "COPY failed"
+    wait
+    exit
+
+fi
+
+if [ -f "GTF/Function/REMcRdy_lm_only/1-0-0-finaltable.csv" ]; then
+   echo "Begin concurrent running of GTF tasks"
+   sh ./mProcess.sh &
+   sh ./mFunction.sh &
+   sh ./mComponent.sh &
+
+   echo "GTF ontologies run in background"
+
+else
+    echo "GTFontologies failed"
+    
+fi
+
+wait
+
+Rscript CompileGTF.R
+wait 
+
+echo "REMcMaster3.sh Finished"
+