diff individuals.Rmd @ 3:5838300fc1aa draft

add expose individuals

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/individuals.Rmd	Mon Apr 02 00:32:04 2018 -0400
@@ -0,0 +1,53 @@
+---
+title: 'Expose data (paired)'
+output: html_document
+---
+
+<style>
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+</style>
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE)
+```
+
+## User input
+
+```{r, echo=FALSE, eval=TRUE}
+##-------- build script files -----------
+
+# build script file: script.sh
+df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
+                sep = '|', header = TRUE)
+
+
+knitr::kable(df)
+```
+
+```{r, echo=FALSE}
+# write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+if (nrow(df) > 0) {
+  for (i in 1:nrow(df)) {
+    tool_output_dir = readLines(df[i, 'tool_output_dir'])[1]
+    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))
+      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']))
+    }
+    # command_line = paste0('cp -r ', full_path, ' paired')
+    # write(command_line, append = TRUE, 
+    #       file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+  }
+}
+```
+
+