added table of contents options to spin.R

R/spinr/spin.R

@@ -15,6 +15,7 @@ Use knitr to spin R documents
 Usage: spin.R [options] <r_script> [<quoted_script_args>]
 
 Options:
+--toc     Add a table of contents
 -c        Cache results
 -e        Show Code
 -w        Show warnings
@@ -100,7 +101,15 @@ opts_chunk$set(
     width=200
 )
 
-knit2html(basename(rmdScript), header=cssHeader)
+knitOptions <- c()
+
+## optionally render toc
+## see http://stackoverflow.com/questions/25872558/generating-a-table-of-contents-toc-when-using-knitrs-spin
+if(spin_opts$toc){
+   knitOptions= c("toc", markdown::markdownHTMLOptions(TRUE))
+}
+
+knit2html(basename(rmdScript), header=cssHeader, options = knitOptions)
 
 ## also remove the .md and the .Rmd files
 if(is.logical(keep_markdown_files) & !keep_markdown_files){

R/spinr/spin_utils.sh

@@ -26,7 +26,7 @@ spinsnip(){
     echo "spining $tmpR..."
 
     shift
-    spinr $tmpR $*
+    spinr -e $tmpR $*
 
 #    rm -r $(dirname $tmpR)
     rm ${tmpR}

bash/bioinfo_utils.sh

@@ -136,8 +136,8 @@ export -f CountFastqGzReads
 
 
 IndexBams(){
-    for bamFile in $1; do
-        sem -j5 -no-notice samtools index $bamFile;
+    for bamFile in $@; do
+        sem -j5 samtools index $bamFile;
     done
     sem -no-notice --wait
 }