From ef85917a7157b7580ef148256433306c511299d3 Mon Sep 17 00:00:00 2001
From: "taha@mkem" <taha@chepec.se>
Date: Wed, 21 May 2014 17:01:12 +0200
Subject: [PATCH] Mainly updates to the way chertex.sh handles Shiny.

---
 chertex.sh      | 16 ++++++++--------
 findlines.sh    | 14 ++++++++++++++
 shiny-matrix.sh |  2 +-
 3 files changed, 23 insertions(+), 9 deletions(-)
 create mode 100755 findlines.sh

diff --git a/chertex.sh b/chertex.sh
index 3ae34bc..1d4102c 100755
--- a/chertex.sh
+++ b/chertex.sh
@@ -64,19 +64,19 @@ if [ $# -eq 1 ]; then
 	
 	
 	#### Special treatment for sample-matrix.Rnw
-   # If $jobname is sample-matrix, run only knitr and markdown, then exit
+   # If $jobname is sample-matrix, restart Shiny and term this script
    if [[ $jobname == "sample-matrix" ]]; then
-	   echo "<cheRTeX> -----------------------------------------------------------"
-      echo "<cheRTeX> sample-matrix: update SHINY, run knit() + markdownToHTML()"
-      echo "<cheRTeX> -----------------------------------------------------------"
+	   echo "<cheRTeX> -------------------------------"
+      echo "<cheRTeX> sample-matrix: restarting Shiny"
+      echo "<cheRTeX> -------------------------------"
       
-      # Before starting new shiny process, kill any previous instances
+      # kill Shiny
       pkill -f "shiny::runApp"
+      # start Shiny
       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')"
+      # terminate this script
       echo "<cheRTeX> Terminating..."
-      /home/taha/chepec/chetex/common/bash/simpledelay.sh 14
+      /home/taha/chepec/chetex/common/bash/simpledelay.sh 4
    	exit 1
    fi
 	
diff --git a/findlines.sh b/findlines.sh
new file mode 100755
index 0000000..b4abc79
--- /dev/null
+++ b/findlines.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+# http://tex.stackexchange.com/a/18776
+# The "holy imagemagick batman" answer :-)
+# run this script like this:
+#   findlines.sh <file>   # without specifying file extension
+# works for two-column pages, not so well for single-column
+
+
+convert $1.pdf -crop 50x100% png:$1
+
+for f in $1-*; do 
+convert $f -flatten -resize 1X1000! -black-threshold 99% -white-threshold 10% -negate -morphology Erode Diamond -morphology Thinning:-1 Skeleton -black-threshold 50% txt:-| \
+sed -e '1d' -e '/black/d' -e 's/^[^,]*,//' -e 's/[(]//g' -e 's/:.*//' -e 's/,/ /g' > $f.txt;
+done
diff --git a/shiny-matrix.sh b/shiny-matrix.sh
index 8444926..06ea49f 100755
--- a/shiny-matrix.sh
+++ b/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...
-nohup R -e "shiny::runApp('~/chepec/chetex/sample-matrix/shinyapp', port = $PORT)"
+nohup R -e "shiny::runApp('/home/taha/chepec/chetex/sample-matrix/shinyapp', port = $PORT)"