diff k2n.R @ 19:ceb96c265bd1 draft

Trying to set environment r lib path dependencies.

--- a/k2n.R	Wed Feb 11 07:32:32 2015 -0500
+++ b/k2n.R	Wed Feb 11 08:05:10 2015 -0500
@@ -1,11 +1,18 @@
+## Setup R error handling to go to stderr
+options( show.error.messages = FALSE, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
 args <- commandArgs(trailingOnly = TRUE)
 
-library(RNAprobR)
+.libPaths(args[1])
+suppressMessages(require(RNAprobR))
 
 # Read inputs
-merged <- args[1]
-unique_barcodes <- args[2]
-output <- args[3]
+merged <- args[2]
+unique_barcodes <- args[3]
+output <- args[4]
 
 k2n_calc( merged, unique_barcodes, output )