Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

changeset 12:bfc6133f3a2b draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 13:48:03 -0400
parents e901094f7e88
children 03893b1ee3ef
files bdss_client.Rmd
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/bdss_client.Rmd	Wed Oct 11 13:36:23 2017 -0400
+++ b/bdss_client.Rmd	Wed Oct 11 13:48:03 2017 -0400
@@ -40,10 +40,10 @@
 # loop through SRA accessions to download and extract reads.
 for(url in urls) {
     bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
-    system(bdss_command, intern = TRUE)
+    system(bdss_command)
 }
 move_files_command = 'find . -type f -print0 | xargs -0 mv -t ./read_files_directory'
-system(move_files_command, intern = TRUE)
+system(move_files_command)
 ```
 
 * `fastq-dump` command