Added support for knitr jobs as well.

chertex.sh will use knitr instead of pgfSweave if it detects a file name ".knitme"
in the directory of the current job. Crude solution, but it should work.

chertex.sh

@@ -60,6 +60,34 @@ if [ $# -eq 1 ]; then
 	simpledelay.sh 2
 	echo "Delay completed"
 
+   ## Handle knitr or pgfSweave jobs separately
+   ## But how should we tell the difference between them?
+   ## There is no obvious way to tell the difference (apart from reading the *.Rnw file)
+   ## IN ALL KNITR DIRECTORIES, CREATE A FILE NAMED: .knitme
+   # If the file .knitme exists in the current directory,
+   # run knitr commands, otherwise run pgfsweave commands
+   echo "--- Looking for .knitme"
+   if [ -e .knitme ]; then
+      # Run knitr commands for this job
+      echo "<cheRTeX> -----------------------"
+      echo "<cheRTeX> This is a job for knitr"
+      echo "<cheRTeX> -----------------------"  
+      
+      # Knit
+	   echo "<cheRTeX> Knitting..."
+      Rscript -e "library(knitr); library(methods); knit('$jobname.$jobfiletype')"
+      
+      # Introduce delay to give time to read Rscript exit status
+   	echo "<cheRTeX> -----------------------"
+   	echo "<cheRTeX> Rscript knitr completed"
+   	echo "<cheRTeX> -----------------------"
+   	simpledelay.sh 4
+   else
+      # Run pgfSweave commands
+      echo "<cheRTeX> ---------------------------"
+      echo "<cheRTeX> This is a job for pgfSweave"
+      echo "<cheRTeX> ---------------------------"
+      
       # Tangle
 	   echo "<cheRTeX> Tangling..."
    	R CMD Stangle $jobname.$jobfiletype
@@ -72,6 +100,7 @@ if [ $# -eq 1 ]; then
    	echo "<cheRTeX> R CMD pgfsweave completed"
    	echo "<cheRTeX> -------------------------"
    	simpledelay.sh 4
+   fi
 		
 	# Run vc script if vc exists in working directory
 	echo "<cheRTeX> Running vc script"
@@ -204,6 +233,11 @@ else
          if [ $cssfiles != 0 ]; then 
             cp /home/taha/chepec/tmp/$tmpdirname/*.css .
          fi
+         # Return .knitme file [empty file used to indicate knitr jobs]
+         knitmefile=`ls -1 /home/taha/chepec/tmp/$tmpdirname/.knitme 2>/dev/null | wc -l`
+         if [ $knitmefile != 0 ]; then 
+            cp /home/taha/chepec/tmp/$tmpdirname/.knitme .
+         fi
       fi
 
 		echo "Terminating..."