The integration between chertex.sh and shiny-matrix.sh now works better.

Running chertex.sh on sample-matrix.Rnw kills previous shiny::runApp() instances,
and creates a new and persistent shiny instance using the nohup command.

chertex.sh

@@ -129,8 +129,9 @@ if [ $# -eq 1 ]; then
       # Old attempts, never worked 
       #PORT=$(</home/taha/chepec/chetex/sample-matrix/shinyapp/shiny.port)
       #bash -c "R -e 'shiny::runApp(\"/home/taha/chepec/chetex/sample-matrix/shinyapp\", port = $PORT)'"
-
-      bash -c "shiny-matrix.sh" & 
+      # Before starting new shiny process, kill any previous instances
+      pkill -f "shiny::runApp"
+      bash -c "/home/taha/chepec/chetex/common/bash/shiny-matrix.sh" & 
       Rscript -e "library(knitr); knit(input='$jobname.Rmd', output='$jobname.md')"
       Rscript -e "library(markdown); markdownToHTML('$jobname.md', '$jobname.html', stylesheet = 'custom.css')"
    fi

shiny-matrix.sh

@@ -21,7 +21,7 @@ echo $PORT > /home/taha/chepec/chetex/sample-matrix/shinyapp/shiny.port
 
 # Run R Shiny app at localhost port
 # Note: this process does not return control to bash...
-R -e "shiny::runApp('~/chepec/chetex/sample-matrix/shinyapp', port = $PORT)"
+nohup R -e "shiny::runApp('~/chepec/chetex/sample-matrix/shinyapp', port = $PORT)"