diff segmentation_sequenza.R @ 6:88e03bac1e36 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"

--- a/segmentation_sequenza.R	Sun Feb 21 12:49:38 2021 +0000
+++ b/segmentation_sequenza.R	Sun Mar 07 12:01:21 2021 +0000
@@ -1,15 +1,17 @@
 # load packages that are provided in the conda env
-options(show.error.messages = F,
-       error = function() {
-           cat(geterrmessage(), file = stderr()); q("no", 1, F)})
-Sys.setenv(TZ = "Pacific/Auckland") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found"
-
+# options(show.error.messages = F,
+#       error = function() {
+#           cat(geterrmessage(), file = stderr()); q("no", 1, F)})
 
 library(optparse)
 library(sequenza)
 library(BiocParallel)
 library(tidyverse)
-
+Sys.setenv(TZ = "Etc/UTC") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found"
+tzdirs <- c(Sys.getenv("TZDIR"), file.path(R.home("share"),
+        "zoneinfo"), "/usr/share/zoneinfo", "/usr/share/lib/zoneinfo",
+        "/usr/lib/zoneinfo", "/usr/local/etc/zoneinfo", "/etc/zoneinfo",
+        "/usr/etc/zoneinfo")
 option_list <- list(
   make_option(
     c("-i", "--input"),