diff segmentation_sequenza.R @ 8:67213c4eefa6 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"

--- a/segmentation_sequenza.R	Sun Mar 07 14:21:06 2021 +0000
+++ b/segmentation_sequenza.R	Sun Mar 07 23:13:08 2021 +0000
@@ -1,10 +1,13 @@
-options(warn = -1)
+options(show.error.messages = F, error = function() {
+        cat(geterrmessage(), file = stderr()); q("no", 1, F) })
 
 # load packages that are provided in the conda env
 library(optparse)
 library(sequenza)
 library(BiocParallel)
 library(tidyverse)
+library(readr)
+
 option_list <- list(
   make_option(
     c("-i", "--input"),
@@ -41,8 +44,14 @@
                "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
                "chr18", "chr19", "chr20", "chr21", "chr22")
 
+Sys.setenv(TZDIR = "/usr/share/zoneinfo/")
+Sys.setenv(TZ = "US/Eastern")
+options(tz = "US/Eastern")
+Sys.timezone(location = TRUE)
+
+
 segfile <- sequenza.extract(data_file,
-                            verbose = TRUE,
+                            verbose = FALSE,
                             chromosome.list = chrom_list)
 
 ## Estimation of cellularity and ploidy