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comparison k2n.R @ 19:ceb96c265bd1 draft

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Trying to set environment r lib path dependencies.
author nikos
date Wed, 11 Feb 2015 08:05:10 -0500
parents 31f25b37187b
children f64937805d0d
comparison
equal deleted inserted replaced
18:c139b9abe064 19:ceb96c265bd1
1 ## Setup R error handling to go to stderr
2 options( show.error.messages = FALSE, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
3
4 # we need that to not crash galaxy with an UTF8 error on German LC settings.
5 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
6
1 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) 7 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
2 args <- commandArgs(trailingOnly = TRUE) 8 args <- commandArgs(trailingOnly = TRUE)
3 9
4 library(RNAprobR) 10 .libPaths(args[1])
11 suppressMessages(require(RNAprobR))
5 12
6 # Read inputs 13 # Read inputs
7 merged <- args[1] 14 merged <- args[2]
8 unique_barcodes <- args[2] 15 unique_barcodes <- args[3]
9 output <- args[3] 16 output <- args[4]
10 17
11 k2n_calc( merged, unique_barcodes, output ) 18 k2n_calc( merged, unique_barcodes, output )