Added support for new sample-matrix markdown source files.

chertex.sh

@@ -89,18 +89,17 @@ if [ $# -eq 1 ]; then
       simpledelay.sh 2
 	   latexmk -pdf -bibtex $jobname
    fi
-	#echo "<cheRTeX> Calling texi2dvi()"
-	#R CMD texi2dvi --pdf --verbose $jobname.tex
-	### Perhaps the choice should be dictated from a command-line argument?
-	
-	# Don't bother with this. Let latexmk take care of cleaning up
-	# Move unnecessary auxiliary files generated
-	#echo "<cheRTeX> _________________________"
-	#echo "<cheRTeX> ========================="
-	#echo "<cheRTeX> Moving auxiliary files..."
-	#mv *.aux logs
-	#mv *.log logs
-	#mv *.out logs	
+
+   ## THIS IS A QUICK-AND-DIRTY FIX FOR SAMPLE-MATRIX
+   # If $jobname is sample-matrix, run knitr and markdown
+   if [[ $jobname == "sample-matrix" ]]; then
+      echo "<cheRTeX> -----------------------------------------------------------"
+      echo "<cheRTeX> sample-matrix detected: running knit() and markdownToHTML()"
+      echo "<cheRTeX> -----------------------------------------------------------"
+      Rscript -e "library(knitr); knit(input='$jobname.Rmd', output='$jobname.md')"
+      Rscript -e "library(markdown); markdownToHTML('$jobname.md', '$jobname.html', stylesheet = 'custom.css')"
+   fi
+
 else
 	# Either no arguments, or more than one argument
 	if [ $# -eq 0 ]; then
@@ -200,6 +199,11 @@ else
          if [ $Rmdfiles != 0 ]; then 
             cp /home/taha/chepec/tmp/$tmpdirname/*.Rmd .
          fi
+         # Return *.css files (css files) [for sample-matrix]
+         cssfiles=`ls -1 /home/taha/chepec/tmp/$tmpdirname/*.css 2>/dev/null | wc -l`
+         if [ $cssfiles != 0 ]; then 
+            cp /home/taha/chepec/tmp/$tmpdirname/*.css .
+         fi
       fi
 
 		echo "Terminating..."