started improved spin shell wrapper

R/spinr/README.md

+A tiny wrapper around knitr::spin to use it from the terminal
+===
+
+To prepare a shell source in the script
+source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/bioinfo_utils.sh 2>&1 2>/dev/null)
+
+
+To use them just source them when needed.
+
+Use the issue tracker to suggest changes or to report problems
+
+Bash
+===
+
+LSF Cluster Utils:
+```
+source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/lsf_utils.sh 2>&1 2>/dev/null)
+```
+
+Tools to simplify bio-dataprocessing in bash
+```
+```
+
+
+R
+===
+
+The R bits are split up into tools for
+* general data handling
+* plotting using ggplot2
+* bioinformatics using various bioconductor packages
+
+```
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/bio/bioinfo_commons.R")
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/datatable_commons.R")
+```
+

R/spinr/spin.R

+#!/usr/bin/env Rscript
+
+# similar http://stackoverflow.com/questions/10943695/what-is-the-knitr-equivalent-of-r-cmd-sweave-myfile-rnw
+
+#http://stackoverflow.com/questions/3433603/parsing-command-line-arguments-in-r-scripts
+#https://github.com/edwindj/docopt.R
+#http://www.slideshare.net/EdwindeJonge1/docopt-user2014
+
+## a thin wrapper around spin to make it more useful with more custom output
+#devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
+
+# load the docopt library
+suppressMessages(library(docopt))
+
+# retrieve and parse the command-line arguments
+doc <- '
+Use knitr to spin R documents
+Usage: spin.R [options] <r_script> [<script_args>...]
+
+Options:
+-c        Cache results
+-e        Show Code
+-w        Show warnings
+-m        Show Messages
+--keep    Keep generated Rmd and md files
+'
+#!docopt(doc, "-w test  a b c ")$keep
+#docopt(doc, "-w test  a b c ")$"-w"
+
+spin_opts <- docopt(doc)
+#print(spin_opts)
+
+r_script <- spin_opts$r_script
+keep_markdown_files <- as.logical(spin_opts$keep)
+
+if(keep_markdown_files){
+    print("keeping markdown files")
+}
+
+if(!file.exists(r_script)){
+     stop(paste("file does not exist\n", doc))
+}
+
+
+require(plyr)
+require(knitr)
+require(stringr)
+
+options(width=150)
+
+#https://groups.google.com/forum/#!topic/knitr/ojcnq5Nm298
+
+## better table css: http://www.stat.ubc.ca/~jenny/STAT545A/topic10_tablesCSS.html
+commandArgs <- function(trailingOnly = FALSE){ return(as.character(spin_opts$script_args)) }
+#print("trimmed args are")
+#print(commandArgs())
+#print("end args")
+
+spin(r_script, knit=F)
+
+rmdScript <- str_replace(r_script, "[.]R$", ".Rmd")
+
+system(paste("mv", rmdScript, "tmp.Rmd"))
+system(paste("cat tmp.Rmd | grep -Ev '^#+$' | grep -Fv '#!/usr/bin/env Rscript' >", basename(rmdScript)))
+file.remove("tmp.Rmd")
+
+cssHeader='
+<style type="text/css">
+  body {
+      max-width: 90%;
+  }
+</style>
+
+
+<!-- add jquery datatable support -->
+<link rel="stylesheet" type="text/css" href="http://cdn.datatables.net/1.10.4/css/jquery.dataTables.css">
+<script type="text/javascript" charset="utf8" src="http://code.jquery.com/jquery-2.1.2.min.js"></script>
+<script type="text/javascript" charset="utf8" src="http://cdn.datatables.net/1.10.4/js/jquery.dataTables.js"></script>
+'
+
+#<!-- add bootstrap support -->
+#<link href="http://maxcdn.bootstrapcdn.com/bootstrap/3.3.1/css/bootstrap.min.css" rel="stylesheet">
+#<script src="http://maxcdn.bootstrapcdn.com/bootstrap/3.3.1/js/bootstrap.min.js"></script>
+
+
+## custom title http://stackoverflow.com/questions/14124022/setting-html-meta-elements-with-knitr
+opts_chunk$set(
+    cache = spin_opts$c,
+    message= spin_opts$m,
+    warning= spin_opts$w,
+    echo= spin_opts$e,
+    fig.width=15,
+    width=200
+)
+
+knit2html(basename(rmdScript), header=cssHeader)
+
+## also remove the .md and the .Rmd files
+if(is.logical(keep_markdown_files) & !keep_markdown_files){
+    file.remove(basename(rmdScript))
+    file.remove(basename(str_replace(r_script, "[.]R$", ".md")))
+}
+

R/spinr/spin_utils.sh

+
+spinr(){
+    ## download if not yet there
+    if [ -z "$(which spin.R)" ]; then
+        wget -P ~/ https://raw.githubusercontent.com/holgerbrandl/themoviedbapi/v1.0/LICENCE.txt
+    fi
+
+    ~/spin.R $*
+}
+
+
+spinsnip(){
+    if [ $# -lt 1 ]; then
+         >&2 echo "Usage: spinsnip <report name> [other args]*"
+        return
+    fi
+
+    reportName=$1
+    tmpR=$(echo $reportName | tr " " "_").R
+
+    ## http://stackoverflow.com/questions/11454343/pipe-output-to-bash-function
+    cat | sed 's/#>/#'"'"'/g'  > $tmpR
+
+    echo "spining $tmpR..."
+
+    shift
+    spinr $tmpR $*
+
+    rm $tmpR
+}
+
+## usage example
+# echo '
+# > # test report
+# 1+1;
+# ggplot(iris, aes(Sepal.Width) + geom_histogram()
+# ' | spinsnip some_report

R/utils/DEPRECATED

+Files in the directory should not be used any longer. Use ../spinr instead
\ No newline at end of file