Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff bdss_client.Rmd @ 21:a709a705ce09 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
author mingchen0919
date Sat, 14 Oct 2017 19:54:57 -0400
parents c2150a0f9c7c
children fd15cf620d5d
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line diff
--- a/bdss_client.Rmd	Sat Oct 14 17:15:39 2017 -0400
+++ b/bdss_client.Rmd	Sat Oct 14 19:54:57 2017 -0400
@@ -10,7 +10,8 @@
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = ECHO
+  echo = ECHO,
+  error=TRUE
 )
 ```
 
@@ -39,9 +40,13 @@
 urls = urls[urls != '']
 # loop through SRA accessions to download and extract reads.
 for(url in urls) {
+    print(url)
     bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
+    print(bdss_command)
     print(system(bdss_command, intern = TRUE))
 }
+# all files that need to be saved should be moved to REPORT_DIR directory
+# print(system('mv read_files_directory REPORT_DIR', intern = TRUE))
 ```