diff individuals.Rmd @ 4:9ff33a3631fa draft

planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty

--- a/individuals.Rmd	Mon Apr 02 00:32:04 2018 -0400
+++ b/individuals.Rmd	Mon Apr 02 08:32:59 2018 -0400
@@ -37,11 +37,15 @@
     full_path = paste0(tool_output_dir, '/', df[i, 'relative_path'])
     if (dir.exists(full_path)) {
       from_files = list.files(full_path, full.names = TRUE)
-      to_files = paste0(Sys.getenv('individual_outputs/'), list.files(full_path))
+      to_files = list.files(full_path)
+      to_files = paste0(individual_outputs_path, to_files)
       file.copy(from = from_files, to = to_files)
     }
     if (file.exists(full_path)) {
-      file.copy(from = full_path, to = paste0(Sys.getenv('individual_outputs/'), df[i, 'relative_path']))
+      # to_files = list.files(full_path)
+      to_file = tail(strsplit(full_path, '/')[[1]], 1)
+      print(to_file)
+      file.copy(from = full_path, to = paste0(individual_outputs_path, to_file))
     }
     # command_line = paste0('cp -r ', full_path, ' paired')
     # write(command_line, append = TRUE,