Mercurial > repos > nturaga > minfi_analyze_tcga
comparison minfi_pipeline.R @ 1:3cd8ea4f7079 draft default tip
planemo upload commit fb90aafc93e5e63acfcdac4c27cfd865cdf06c5a-dirty
| author | nturaga |
|---|---|
| date | Tue, 19 Apr 2016 12:21:01 -0400 |
| parents | 8b26eeb2da29 |
| children |
comparison
equal
deleted
inserted
replaced
| 0:8b26eeb2da29 | 1:3cd8ea4f7079 |
|---|---|
| 1 # setup R error handling to go to stderr | 1 # setup R error handling to go to stderr |
| 2 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) | 2 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) |
| 3 | 3 |
| 4 # we need that to not crash galaxy with an UTF8 error on German LC settings. | 4 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
| 5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | 5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
| 6 | |
| 7 install.packages('getopt', repos='http://cran.us.r-project.org') | |
| 6 | 8 |
| 7 library("getopt") | 9 library("getopt") |
| 8 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) | 10 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) |
| 9 args <- commandArgs(trailingOnly = TRUE) | 11 args <- commandArgs(trailingOnly = TRUE) |
| 10 | 12 |